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Found 1 Document (0.679 seconds)

BMRB: 11570

2RUI

Solution Structure of the Bacillus anthracis Sortase A-substrate Complex

Authors

Chan, A.H., Yi, S., Jung, M.E., Clubb, R.T.

Assembly

SrtA AX bocLPAT

Entity

1. BaSrtA (polymer, Thiol state: all disulfide bound), 158 monomers, 17086.17 Da Detail

GSHMDASKID QPDLAEVANA SLDKKQVIGR ISIPSVSLEL PVLKSSTEKN LLSGAATVKE NQVMGKGNYA LAGHNMSKKG VLFSDIASLK KGDKIYLYDN ENEYEYAVTG VSEVTPDKWE VVEDHGKDEI TLITCVSVKD NSKRYVVAGD LVGTKAKK

2. Boc-LPAT* (polymer, Thiol state: all disulfide bound), 5 monomers, 502.6669 Da Detail

XLPAX

Total weight

17588.836 Da

Max. entity weight

17086.17 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS135:SG	2:B275:CYS

Source organism

Bacillus anthracis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.3 %, Completeness: 88.9 %, Completeness (bb): 94.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.9 % (1617 of 1818)	87.4 % (822 of 941)	90.6 % (642 of 709)	91.1 % (153 of 168)
Backbone	94.1 % (900 of 956)	94.5 % (311 of 329)	94.3 % (444 of 471)	92.9 % (145 of 156)
Sidechain	85.0 % (859 of 1011)	83.5 % (511 of 612)	87.9 % (340 of 387)	66.7 % (8 of 12)
Aromatic	57.3 % (47 of 82)	58.5 % (24 of 41)	57.5 % (23 of 40)	0.0 % (0 of 1)
Methyl	93.9 % (184 of 196)	95.9 % (94 of 98)	91.8 % (90 of 98)

1. BaSrtA

GSHMDASKID QPDLAEVANA SLDKKQVIGR ISIPSVSLEL PVLKSSTEKN LLSGAATVKE NQVMGKGNYA LAGHNMSKKG VLFSDIASLK KGDKIYLYDN ENEYEYAVTG VSEVTPDKWE VVEDHGKDEI TLITCVSVKD NSKRYVVAGD LVGTKAKK

2. Boc-LPAT*

XLPAX

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
8	Boc-LPAT	natural abundance		2.6 mM
9	sodium phosphate	natural abundance	buffer	50 mM
10	sodium azide	natural abundance		0.01 %
11	D2O	[U-2H]	solvent	100 %

Protein Blocks Logo

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

Release date

2015-09-09

Citation

Structure of the Bacillus anthracis Sortase-Substrate Complex Reveals Important Roles of the N-terminus Tail in Transpeptidation Reaction
Chan, A.H., Yi, S., Jung, M.E., Clubb, R.T.
J. Biol. Chem.

Related entities 1. BaSrtA, : 2 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
8	Boc-LPAT	natural abundance		2.6 mM
9	sodium phosphate	natural abundance	buffer	50 mM
10	sodium azide	natural abundance		0.01 %
11	D2O	[U-2H]	solvent	100 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

4 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

5 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

6 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
8	Boc-LPAT	natural abundance		2.6 mM
9	sodium phosphate	natural abundance	buffer	50 mM
10	sodium azide	natural abundance		0.01 %
11	D2O	[U-2H]	solvent	100 %

9 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
8	Boc-LPAT	natural abundance		2.6 mM
9	sodium phosphate	natural abundance	buffer	50 mM
10	sodium azide	natural abundance		0.01 %
11	D2O	[U-2H]	solvent	100 %

12 3D HNHB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

13 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
7	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
8	Boc-LPAT	natural abundance		2.6 mM
9	sodium phosphate	natural abundance	buffer	50 mM
10	sodium azide	natural abundance		0.01 %
11	D2O	[U-2H]	solvent	100 %

14 3D HCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

15 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	BaSrtA	[U-100% 13C; U-100% 15N]	protein	2.6 mM
2	Boc-LPAT	natural abundance		2.6 mM
3	sodium phosphate	natural abundance	buffer	50 mM
4	sodium azide	natural abundance		0.01 %
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_11570_2rui.nef
Input source #2: Coordindates	2rui.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:135:CYS:SG	2:5:B27:SG	unknown	unknown	n/a

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)
2:1:BOC:C	2:2:LEU:N	unknown	unknown	n/a
2:4:ALA:C	2:5:B27:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	701	BOC	TERT-BUTYL HYDROGEN CARBONATE	Coordinates
B	705	B27	(2R,3S) 3-amino-4-mercapto-2-butanol	Assigned chemical shifts, Coordinates

Sequence alignments

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

------60--------70--------80--------90-------100-------110-------120-------130-------140-------150--
GSHMDASKIDQPDLAEVANASLDKKQVIGRISIPSVSLELPVLKSSTEKNLLSGAATVKENQVMGKGNYALAGHNMSKKGVLFSDIASLKKGDKIYLYDN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSHMDASKIDQPDLAEVANASLDKKQVIGRISIPSVSLELPVLKSSTEKNLLSGAATVKENQVMGKGNYALAGHNMSKKGVLFSDIASLKKGDKIYLYDN
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----160-------170-------180-------190-------200-------210
ENEYEYAVTGVSEVTPDKWEVVEDHGKDEITLITCVSVKDNSKRYVVAGDLVGTKAKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ENEYEYAVTGVSEVTPDKWEVVEDHGKDEITLITCVSVKDNSKRYVVAGDLVGTKAKK
-------110-------120-------130-------140-------150--------

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

-----
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Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	158	0	0	100.0
B	B	5	0	0	100.0

Content subtype: combined_11570_2rui.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1608		96.8 (chain: A, length: 158), 80.0 (chain: B, length: 5)
1	Distance restraints	CNS/XPLOR_distance_constraints_7	Warning	3395 (1)	noe	94.9 (chain: A, length: 158)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	316 (316)	.	98.7 (chain: A, length: 158)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	151 (151)	.	72.2 (chain: A, length: 158)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 96.8%
  - Entity_assembly_ID: B, Chain length: 5, Sequence coverage: 80.0%
- Total number of assignments
  - ¹H chemical shifts: 814
  - ¹³C chemical shifts: 642
  - ¹⁵N chemical shifts: 152
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
71	ASN	CG	176.896
82	ARG	CZ	159.208
102	ASN	CG	174.468
113	ASN	CG	177.966
120	ASN	CG	176.894
152	ASN	CG	177.24
154	ASN	CG	175.517

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	924	796	86.1
¹³C chemical shifts	695	635	91.4
¹⁵N chemical shifts	168	152	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	324	305	94.1
¹³C chemical shifts	316	298	94.3
¹⁵N chemical shifts	154	143	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	600	491	81.8
¹³C chemical shifts	379	337	88.9
¹⁵N chemical shifts	14	9	64.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	92	93.9
¹³C chemical shifts	98	92	93.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	24	58.5
¹³C chemical shifts	40	23	57.5
¹⁵N chemical shifts	1	0	0.0

Comp_index_ID	Comp_ID
701	BOC
705	B27

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	14	82.4
¹³C chemical shifts	14	0	0.0
¹⁵N chemical shifts	2	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	3	60.0
¹³C chemical shifts	6	0	0.0
¹⁵N chemical shifts	2	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	12	11	91.7
¹³C chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	3	3	100.0
¹³C chemical shifts	3	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_7
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 94.9%
- Total number of restraints: 3351
- Weight of restraints: 1.0 (3351)
- Potential type of restraints: square-well-parabolic (3351)
- Range of distance target values: 2.19, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 98.7%
- Total number of restraints: 316
- Total number of restraints per polymer type: 316
- Weight of restraints: 1.0 (316)
- Potential type of restraints: square-well-parabolic (316)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 72.2%

------60--------70--------80--------90-------100-------110-------120-------130-------140-------150--
GSHMDASKIDQPDLAEVANASLDKKQVIGRISIPSVSLELPVLKSSTEKNLLSGAATVKENQVMGKGNYALAGHNMSKKGVLFSDIASLKKGDKIYLYDN
   ||||||||  |||| |||  ||    ||||||||||| ||  ||||  |||   |||||||||||| |||    |||||||| ||||||||||||||
...MDASKIDQ..LAEV.NAS..KK....RISIPSVSLEL.VL..STEK..LSG...VKENQVMGKGNY.LAG....KKGVLFSD.ASLKKGDKIYLYDN

-----160-------170-------180-------190-------200-------210
ENEYEYAVTGVSEVTPDKWEVVEDHGKDEITLITCVSVKDNSKRYVVAGDLVGTKAKK
|||||||||||||   ||   || ||||||||||    |       ||||||||||||
ENEYEYAVTGVSE...DK...VE.HGKDEITLIT....K.......VAGDLVGTKAKK

Total number of restraints: 151
Potential type of restraints: undefined (151)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords Bacillus anthracis, Complex, Sortase, SrtA, Transpeptidase

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Found 1 Document (0.679 seconds)

BMRB: 11570

Sample #1

Sample #2

Related entities 1. BaSrtA, : 2 entities Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 5 contents Detail