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BMRB: 16811

2KW8

Solution Structure of Bacillus anthracis Sortase A (SrtA) Transpeptidase

Authors

Weiner, E.M., Robson, S.A., Marohn, M., Clubb, R.T.

Assembly

SrtA

Entity

1. SrtA (polymer, Thiol state: all free), 158 monomers, 17086.17 Da Detail

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

Formula weight

17086.17 Da

Source organism

Bacillus anthracis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.3 %, Completeness: 86.6 %, Completeness (bb): 91.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.6 % (1546 of 1785)	85.5 % (790 of 924)	87.3 % (607 of 695)	89.8 % (149 of 166)
Backbone	91.1 % (856 of 940)	90.1 % (292 of 324)	91.3 % (422 of 462)	92.2 % (142 of 154)
Sidechain	82.7 % (820 of 991)	82.0 % (492 of 600)	84.7 % (321 of 379)	58.3 % (7 of 12)
Aromatic	68.3 % (56 of 82)	70.7 % (29 of 41)	65.0 % (26 of 40)	100.0 % (1 of 1)
Methyl	95.8 % (182 of 190)	96.8 % (92 of 95)	94.7 % (90 of 95)

1. SrtA

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

Show sample condition

Sample #1

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

#	Name	Isotope labeling	Concentration
1	SrtA	[U-100% 15N]	4 mM
2	MES	natural abundance	10 mM
3	Bis-Tris	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	7 %

Sample #2

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

#	Name	Isotope labeling	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

Sample #3

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

#	Name	Isotope labeling	Concentration
11	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
12	MES	natural abundance	10 mM
13	Bis-Tris	natural abundance	20 mM
14	H2O	natural abundance	93 %
15	D2O	natural abundance	7 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.35 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 40 models in PDB: 2KW8, Strand ID: A Detail

Release date

2010-05-27

Citation

The Sortase A enzyme that attaches proteins to the cell wall of Bacillus anthracis contains an unusual active site architecture
Weiner, E.M., Robson, S., Marohn, M., Clubb, R.T.
J. Biol. Chem. (2010), 285, 23433-23443, PubMed 20489200 , DOI 10.1074/jbc.M110.135434 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 26510 released on 2015-02-24
Title The Sortase A Enzyme That Attaches Proteins to the Cell Wall of Bacillus anthracis Contains an Unusual Active Site Architecture

Related entities 1. SrtA, : 1 : 1 : 47 entities Detail

Experiments performed 21 experiments Detail

1 2D 1H-15N HSQC

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	Concentration
1	SrtA	[U-100% 15N]	4 mM
2	MES	natural abundance	10 mM
3	Bis-Tris	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	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	Concentration
11	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
12	MES	natural abundance	10 mM
13	Bis-Tris	natural abundance	20 mM
14	H2O	natural abundance	93 %
15	D2O	natural abundance	7 %

3 2D 1H-13C HSQC

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

4 3D CBCA(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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

5 3D C(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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

6 3D HNCO

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

7 3D HNCA

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

8 3D HNCACB

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

9 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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
11	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
12	MES	natural abundance	10 mM
13	Bis-Tris	natural abundance	20 mM
14	H2O	natural abundance	93 %
15	D2O	natural abundance	7 %

11 3D HNHA

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

12 3D 1H-15N NOESY

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

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

#	Name	Isotope labeling	Concentration
11	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
12	MES	natural abundance	10 mM
13	Bis-Tris	natural abundance	20 mM
14	H2O	natural abundance	93 %
15	D2O	natural abundance	7 %

14 3D HNHB

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

15 3D HCCH-COSY

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

16 3D HCACO

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

17 4D 15N-13C HMQC-NOESY-HSQC

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

18 2D (HB)CB(CGCDCE)HE

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

19 2D (HB)CB(CGCD)HD

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

20 2D 1H-15N HSQC

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	Concentration
6	SrtA	[U-100% 13C; U-100% 15N]	2.5 mM
7	MES	natural abundance	10 mM
8	Bis-Tris	natural abundance	20 mM
9	H2O	natural abundance	93 %
10	D2O	natural abundance	7 %

21 2D 1H-15N HSQC NOE with interleaved presat and no sat

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	Concentration
1	SrtA	[U-100% 15N]	4 mM
2	MES	natural abundance	10 mM
3	Bis-Tris	natural abundance	20 mM
4	H2O	natural abundance	93 %
5	D2O	natural abundance	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_16811_2kw8.nef
Input source #2: Coordindates	2kw8.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	None
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)

None

Non-standard residues

None

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--------

Chain assignments

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

Content subtype: combined_16811_2kw8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1594		93.0 (chain: A, length: 158)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3860 (1)	noe	92.4 (chain: A, length: 158)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_7	OK	231 (231)	.	92.4 (chain: A, length: 158)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	116 (116)	.	58.2 (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: 93.0%
- Total number of assignments
  - ¹H chemical shifts: 856
  - ¹³C chemical shifts: 592
  - ¹⁵N chemical shifts: 146
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
105	SER	HG	5.255

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	924	779	84.3
¹³C chemical shifts	695	592	85.2
¹⁵N chemical shifts	168	146	86.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	324	298	92.0
¹³C chemical shifts	316	282	89.2
¹⁵N chemical shifts	154	140	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	600	481	80.2
¹³C chemical shifts	379	310	81.8
¹⁵N chemical shifts	14	6	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	91	92.9
¹³C chemical shifts	98	89	90.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	27	65.9
¹³C chemical shifts	40	26	65.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 92.4%
- Total number of restraints: 3860
- Weight of restraints: 1.0 (3860)
- Potential type of restraints: square-well-parabolic (3860)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_7
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 92.4%
- Total number of restraints: 231
- Total number of restraints per polymer type: 231
- Weight of restraints: 1.0 (231)
- Potential type of restraints: square-well-parabolic (231)
- 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: 58.2%

------60--------70--------80--------90-------100-------110-------120-------130-------140-------150--
GSHMDASKIDQPDLAEVANASLDKKQVIGRISIPSVSLELPVLKSSTEKNLLSGAATVKENQVMGKGNYALAGHNMSKKGVLFSDIASLKKGDKIYLYDN
             |  | ||   | ||||||||||||||| ||  |   ||| | ||| ||||||||||||||   ||||||  | ||| ||  | |   
.............L..V.NA...K.QVIGRISIPSVSLEL.VL..S...NLL.G.ATV.ENQVMGKGNYALAG...SKKGVL..D.ASL.KG..I.L...

-----160-------170-------180-------190-------200-------210
ENEYEYAVTGVSEVTPDKWEVVEDHGKDEITLITCVSVKDNSKRYVVAGDLVGTKAKK
|| ||||||| || | ||   ||||||||||             |||||  ||||  |
EN.YEYAVTG.SE.T.DK...VEDHGKDEIT.............YVVAG..VGTK..K

Total number of restraints: 116
Potential type of restraints: undefined (116)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords Sortase, SrtA, transpeptidase

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Found 1 Document (0.99 seconds)

BMRB: 16811

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. SrtA, : 1 : 1 : 47 entities Detail

Experiments performed 21 experiments Detail

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NMR combined restraints 5 contents Detail