BMRBj - BMREntryMaster

Found 1 Document (1.532 seconds)

BMRB: 34471

8GPC

Haddock model of NDM-1/morin complex

Authors

Riviere, G., Oueslati, S., Gayral, M., Crechet, J.B., Nhiri, N., Jacquet, E., Cintrat, J.C., Giraud, F., van Heijenoort, C., Lescop, E., Pethe, S., Iorga, B.I., Naas, T., Guittet, E., Morellet, N.

Assembly

Metallo beta lactamase NDM-1

Entity

1. Metallo beta lactamase NDM-1, entity 1 (polymer), 227 monomers, 23950.72 Da Detail

DQRFGDLVFR QLAPNVWQHT SYLDMPGFGA VASNGLIVRD GGRVLVVDTA WTDDQTAQIL NWIKQEINLP VALAVVTHAH QDKMGGMDAL HAAGIATYAN ALSNQLAPQE GMVAAQHSLT FAANGWVEPA TAPNFGPLKV FYPGPGHTSD NITVGIDGTD IAFGGCLIKD SKAKSLGNLG DADTEHYAAS ARAFGAAFPK ASMIVMSHSA PDSRAAITHT ARMADKL

2. Metallo beta lactamase NDM-1, entity ZN (non-polymer), 65.409 × 2 Da
3. Metallo beta lactamase NDM-1, entity MRI (non-polymer), 302.236 Da

Total weight

24383.775 Da

Max. entity weight

23950.72 Da

Entity Connection

na 5 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS78:NE2	2:ZN1:ZN
2	na	sing	1:HIS80:ND1	2:ZN1:ZN
3	na	sing	1:HIS147:NE2	2:ZN1:ZN
4	na	sing	1:HIS208:NE2	2:ZN1:ZN
5	na	sing	2:ZN1:ZN	3:MRI1:OAC

Source organism

Klebsiella pneumoniae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 43.1 %, Completeness (bb): 75.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	43.1 % (1069 of 2480)	20.7 % (261 of 1258)	61.8 % (603 of 975)	83.0 % (205 of 247)
Backbone	75.1 % (1006 of 1340)	47.2 % (219 of 464)	88.2 % (582 of 660)	94.9 % (205 of 216)
Sidechain	16.9 % (227 of 1346)	5.4 % (43 of 794)	35.3 % (184 of 521)	0.0 % (0 of 31)
Aromatic	0.0 % (0 of 206)	0.0 % (0 of 103)	0.0 % (0 of 99)	0.0 % (0 of 4)
Methyl	26.1 % (71 of 272)	14.7 % (20 of 136)	37.5 % (51 of 136)

1. entity 1

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.05), Details 320 uM [U-13C; U-15N] NDM-1, 1280 uM morin, 0.1 mM Bis-tris, 150 mM sodium chloride, 2.5 % DMSO, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NDM-1	[U-13C; U-15N]	320 uM
2	morin	natural abundance	1280 uM
3	Bis-tris	natural abundance	0.1 mM
4	sodium chloride	natural abundance	150 mM
5	DMSO	natural abundance	2.5 %

Protein Blocks Logo

Calculated from 56 models in PDB: 6TT8, Strand ID: A Detail

Release date

2020-07-13

Citation

NDM-1: a local clone emerges with worldwide aspirations
Marra, A.
Future Microbiol. (2011), 6, 137-141, PubMed 21366414 , DOI 10.2217/fmb.10.171 , Abstract

Related entities 1. Metallo beta lactamase NDM-1, entity 1, : 1 : 100 : 16 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0 (±0.05), Details 320 uM [U-13C; U-15N] NDM-1, 1280 uM morin, 0.1 mM Bis-tris, 150 mM sodium chloride, 2.5 % DMSO, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	NDM-1	[U-13C; U-15N]	320 uM
2	morin	natural abundance	1280 uM
3	Bis-tris	natural abundance	0.1 mM
4	sodium chloride	natural abundance	150 mM
5	DMSO	natural abundance	2.5 %

2 2D 1H-15N HSQC

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NDM-1	[U-13C; U-15N]	320 uM
2	morin	natural abundance	1280 uM
3	Bis-tris	natural abundance	0.1 mM
4	sodium chloride	natural abundance	150 mM
5	DMSO	natural abundance	2.5 %

3 3D HNCO

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NDM-1	[U-13C; U-15N]	320 uM
2	morin	natural abundance	1280 uM
3	Bis-tris	natural abundance	0.1 mM
4	sodium chloride	natural abundance	150 mM
5	DMSO	natural abundance	2.5 %

4 3D HNCA

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NDM-1	[U-13C; U-15N]	320 uM
2	morin	natural abundance	1280 uM
3	Bis-tris	natural abundance	0.1 mM
4	sodium chloride	natural abundance	150 mM
5	DMSO	natural abundance	2.5 %

5 3D HNCACB

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NDM-1	[U-13C; U-15N]	320 uM
2	morin	natural abundance	1280 uM
3	Bis-tris	natural abundance	0.1 mM
4	sodium chloride	natural abundance	150 mM
5	DMSO	natural abundance	2.5 %

6 3D HN(CO)CA

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NDM-1	[U-13C; U-15N]	320 uM
2	morin	natural abundance	1280 uM
3	Bis-tris	natural abundance	0.1 mM
4	sodium chloride	natural abundance	150 mM
5	DMSO	natural abundance	2.5 %

7 3D HN(COCA)CB

Instrument

Bruker AVANCE II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	NDM-1	[U-13C; U-15N]	320 uM
2	morin	natural abundance	1280 uM
3	Bis-tris	natural abundance	0.1 mM
4	sodium chloride	natural abundance	150 mM
5	DMSO	natural abundance	2.5 %

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr34471_3.str
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)
1:78:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:80:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:147:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:208:HIS:NE2	3:1:ZN:ZN	unknown	unknown	n/a
2:1:ZN:ZN	4:1:MRI:OAC	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr34471_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	993		97.8 (chain: 1, length: 227)
1	Chemical shift references	chem_shift_reference_1	Warning	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 227, Sequence coverage: 97.8%
- Total number of assignments
  - ¹³C chemical shifts: 581
  - ¹H chemical shifts: 206
  - ¹⁵N chemical shifts: 206
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	975	581	59.6
¹H chemical shifts	1258	206	16.4
¹⁵N chemical shifts	247	206	83.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	454	421	92.7
¹H chemical shifts	464	206	44.4
¹⁵N chemical shifts	216	206	95.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	521	160	30.7
¹H chemical shifts	794	0	0.0
¹⁵N chemical shifts	31	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	143	34	23.8
¹H chemical shifts	143	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	99	0	0.0
¹H chemical shifts	103	0	0.0
¹⁵N chemical shifts	4	0	0.0

Keywords Haddock, METAL BINDING PROTEIN, New-Delhi Metallo-beta-lactamase-1, antimicrobial resistance, complex, inhibitor, morin

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Found 1 Document (1.532 seconds)

BMRB: 34471

Sample

Related entities 1. Metallo beta lactamase NDM-1, entity 1, : 1 : 100 : 16 entities Detail

Experiments performed 7 experiments Detail

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Chemical shift validation 5 contents Detail