BMRBj - BMREntryMaster

Found 1 Document (1.085 seconds)

BMRB: 19048

2M5D

Solution Structure of the Bacillus cereus Metallo-Beta-Lactamase BcII in Complex with R-Thiomandelic Acid

Authors

Karsisiotis, A., Damblon, C.F., Roberts, G.CK.

Assembly

BcII

Entity

1. BcII (polymer, Thiol state: all other bound), 227 monomers, 24960.21 Da Detail

SQKVEKTVIK NETGTISISQ LNKNVWVHTE LGSFNGEAVP SNGLVLNTSK GLVLVDSSWD DKLTKELIEM VEKKFQKRVT DVIITHAHAD RIGGIKTLKE RGIKAHSTAL TAELAKKNGY EEPLGDLQTV TNLKFGNMKV ETFYPGKGHT EDNIVVWLPQ YNILVGGCLV KSTSAKDLGN VADAYVNEWS TSIENVLKRY RNINAVVPGH GEVGDKGLLL HTLDLLK

2. 3-(2-aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide (non-polymer, Thiol state: not present), 311.421 Da
3. ZINC ION (non-polymer, Thiol state: not present), 65.409 × 2 Da

Total weight

25402.451 Da

Max. entity weight

24960.21 Da

Entity Connection

na 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS168:SG	3:ZN1:ZN

Source organism

Bacillus cereus

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete1

Sequence coverage: 99.1 %, Completeness: 83.1 %, Completeness (bb): 77.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.1 % (2190 of 2634)	93.8 % (1275 of 1360)	79.6 % (817 of 1027)	39.7 % (98 of 247)
Backbone	77.7 % (1050 of 1352)	97.4 % (457 of 469)	75.3 % (498 of 661)	42.8 % (95 of 222)
Sidechain	90.1 % (1341 of 1489)	91.8 % (818 of 891)	90.8 % (520 of 573)	12.0 % (3 of 25)
Aromatic	87.2 % (136 of 156)	100.0 % (78 of 78)	77.0 % (57 of 74)	25.0 % (1 of 4)
Methyl	99.3 % (300 of 302)	99.3 % (150 of 151)	99.3 % (150 of 151)

1. BcII

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.4, Details BcII(15N)-R-Thiomandelic Acid ~1mM in 20 mM MES, 100 mM NaCl, 0.2mM ZnCl2, pH 6.4, in H2O(90%)/D2O(10%)

#	Name	Isotope labeling	Concentration
1	BcII	[U-99% 15N]	1 mM
2	R-Thiomandelic Acid	natural abundance	1 mM
3	MES	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.4, Details BcII(13C,15N)-R-Thiomandelic Acid ~1mM in 20 mM MES, 100 mM NaCl, 0.2mM ZnCl2, pH 6.4, in H2O(90%)/D2O(10%)

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Chem. Shift Complete2

Sequence coverage: 99.6 %, Completeness: 74.6 %, Completeness (bb): 71.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.6 % (3930 of 5268)	91.8 % (2498 of 2720)	53.5 % (1099 of 2054)	67.4 % (333 of 494)
Backbone	71.0 % (1919 of 2704)	96.6 % (906 of 938)	53.6 % (708 of 1322)	68.7 % (305 of 444)
Sidechain	76.5 % (2278 of 2978)	89.3 % (1592 of 1782)	57.4 % (658 of 1146)	56.0 % (28 of 50)
Aromatic	59.9 % (187 of 312)	76.9 % (120 of 156)	41.9 % (62 of 148)	62.5 % (5 of 8)
Methyl	80.6 % (487 of 604)	98.7 % (298 of 302)	62.6 % (189 of 302)

1. BcII

Show sample condition

Sample #1

#	Name	Isotope labeling	Concentration
1	BcII	[U-99% 15N]	1 mM
2	R-Thiomandelic Acid	natural abundance	1 mM
3	MES	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M5D, Strand ID: A Detail

Release date

2013-08-13

Citation

Complete ¹H, ¹⁵N, and ¹³C resonance assignments of Bacillus cereus metallo-β-lactamase and its complex with the inhibitor R-thiomandelic acid
Karsisiotis, A., Damblon, C.F., Roberts, G.CK.
Biomol. NMR Assign. (2014), 8, 313-318, PubMed 23838816 , DOI 10.1007/s12104-013-9507-1 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 19047 released on 2013-08-13
Title Solution Structure of the Bacillus cereus Metallo-Beta-Lactamase BcII

Related entities 1. BcII, : 1 : 14 : 1 : 30 : 72 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.4, Details BcII(15N)-R-Thiomandelic Acid ~1mM in 20 mM MES, 100 mM NaCl, 0.2mM ZnCl2, pH 6.4, in H2O(90%)/D2O(10%)

#	Name	Isotope labeling	Concentration
1	BcII	[U-99% 15N]	1 mM
2	R-Thiomandelic Acid	natural abundance	1 mM
3	MES	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.4, Details BcII(13C,15N)-R-Thiomandelic Acid ~1mM in 20 mM MES, 100 mM NaCl, 0.2mM ZnCl2, pH 6.4, in H2O(90%)/D2O(10%)

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

3 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz Bruker Avance DRX 800 MHz with cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

4 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz Bruker Avance DRX 800 MHz with cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

7 3D HNCA

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

8 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 3D HNCO

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz Bruker Avance DRX 600 MHz with cryoprobe

Sample

#	Name	Isotope labeling	Concentration
1	BcII	[U-99% 15N]	1 mM
2	R-Thiomandelic Acid	natural abundance	1 mM
3	MES	natural abundance	20 mM
4	sodium chloride	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

13 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz Bruker Avance DRX 800 MHz with cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

14 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz Bruker Avance DRX 800 MHz with cryoprobe

Sample

#	Name	Isotope labeling	Concentration
7	BcII	[U-99% 13C; U-99% 15N]	1 mM
8	R-Thiomandelic Acid	natural abundance	1 mM
9	MES	natural abundance	20 mM
10	sodium chloride	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19048_2m5d.nef
Input source #2: Coordindates	2m5d.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:149:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:90:ASP:OD2	2:2:ZN:ZN	unknown	unknown	n/a
2:2:ZN:ZN	3:1:RTD:S1	unknown	unknown	n/a
1:168:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:88:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:86:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
2:1:ZN:ZN	3:1:RTD:S1	unknown	unknown	n/a
1:210:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	RTD	(2R)-phenyl(sulfanyl)ethanoic acid	Distance restraints
C	1	ZN	ZINC ION	Distance restraints
C	2	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
SQKVEKTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SQKVEKTVIKNETGTISISQLNKNVWVHTELGSFNGEAVPSNGLVLNTSKGLVLVDSSWDDKLTKELIEMVEKKFQKRVTDVIITHAHADRIGGIKTLKE

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
RGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RGIKAHSTALTAELAKKNGYEEPLGDLQTVTNLKFGNMKVETFYPGKGHTEDNIVVWLPQYNILVGGCLVKSTSAKDLGNVADAYVNEWSTSIENVLKRY

-------210-------220-------
RNINAVVPGHGEVGDKGLLLHTLDLLK
|||||||||||||||||||||||||||
RNINAVVPGHGEVGDKGLLLHTLDLLK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	227	0	0	100.0

Content subtype: combined_19048_2m5d.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2010		99.1 (chain: A, length: 227)
2	Assigned chemical shifts	assigned_chem_shift_list_2	Warning	1427		99.1 (chain: A, length: 227)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	9102 (1)	noe	99.1 (chain: A, length: 227)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	14 (1)	undefined	2.6 (chain: A, length: 227), 100.0 (chain: B, length: 1), 50.0 (chain: C, length: 2)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 227, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 1280
  - ¹³C chemical shifts: 730
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
Saveframe: assigned_chem_shift_list_2
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 227, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 1196
  - ¹⁵N chemical shifts: 231
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
28	HIS	HE2	10.68
48	THR	HG1	5.69
80	THR	HG1	6.293
108	THR	HG1	6.776
142	THR	HG1	5.54
192	SER	HG	5.319
210	HIS	HD1	13.346
222	THR	HG1	5.277

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1360	1272	93.5
¹³C chemical shifts	1027	730	71.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	469	455	97.0
¹³C chemical shifts	454	223	49.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	891	817	91.7
¹³C chemical shifts	573	507	88.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	153	151	98.7
¹³C chemical shifts	153	151	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	77	98.7
¹³C chemical shifts	74	54	73.0

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
48	THR	HG1	5.671
80	THR	HG1	6.266
222	THR	HG1	5.284

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1360	1193	87.7
¹⁵N chemical shifts	252	231	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	469	445	94.9
¹⁵N chemical shifts	222	207	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	891	748	84.0
¹⁵N chemical shifts	30	24	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	153	151	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	39	50.0
¹⁵N chemical shifts	4	4	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 227, Sequence coverage: 99.1%
- Total number of restraints: 8970
- Weight of restraints: 1.0 (8970)
- Potential type of restraints: upper-bound-parabolic (8970)
- Range of distance target values: 2.32, 6.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 227, Sequence coverage: 2.6%
    - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
    - Entity_assembly_ID: C, Chain length: 2, Sequence coverage: 50.0%
  - Total number of restraints: 14
  - Weight of restraints: 1.0 (14)
  - Potential type of restraints: upper-bound-parabolic (14)
  - Range of distance target values: 2.2, 3.85 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
  - Distance restraints on contact map

Keywords Bacillus cereus, BcII, broad spectrum inhibitor, complex, mercaptocarboxylate inhibitor, Metallo-Beta-Lactamase, R-Thiomandelic Acid, Solution NMR

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.085 seconds)

BMRB: 19048

Sample #1

Sample #2

Sample #1

Sample #2

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. BcII, : 1 : 14 : 1 : 30 : 72 entities Detail

Experiments performed 14 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail