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- PDB-4iyh: The crystal structure of a secreted protein EsxB (SeMet-labeled, ... -

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Basic information

Entry
Database: PDB / ID: 4iyh
TitleThe crystal structure of a secreted protein EsxB (SeMet-labeled, C-term. His-Tagged) from Bacillus anthracis str. Sterne
ComponentsSecreted protein EsxB
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Protein Structure Initiative / Midwest Center For Structural Genomics / MCSG
Function / homology
Function and homology information


HP0062-like domain superfamily / HP0062-like domain / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / ESAT-6-like protein / ESAT-6-like protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.881 Å
AuthorsFan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a secreted protein EsxB (SeMet-labeled, C-term. His-Tagged) from Bacillus anthracis str. Sterne
Authors: Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Secreted protein EsxB
B: Secreted protein EsxB
C: Secreted protein EsxB
D: Secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,65718
Polymers44,6044
Non-polymers1,05314
Water2,900161
1
A: Secreted protein EsxB
B: Secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8549
Polymers22,3022
Non-polymers5517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-89 kcal/mol
Surface area8750 Å2
MethodPISA
2
C: Secreted protein EsxB
D: Secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8039
Polymers22,3022
Non-polymers5017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-94 kcal/mol
Surface area8720 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16970 Å2
ΔGint-197 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.337, 77.337, 71.226
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Secreted protein EsxB


Mass: 11151.069 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: Bacillus anthracis / Plasmid: pMCSG26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81R67, UniProt: A0A6L7HJC4*PLUS

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M Na2HPO4:Citric Acid, 2.0M Ammonium Sulfate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2010 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.52
ReflectionResolution: 1.88→49 Å / Num. all: 38708 / Num. obs: 38708 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.9
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1928 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.881→48.792 Å / σ(F): 1.96 / Phase error: 16.08 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1615 1939 5.01 %random
Rwork0.1411 ---
obs0.145 38682 99.97 %-
all-38682 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.881→48.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 60 161 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062616
X-RAY DIFFRACTIONf_angle_d0.8063500
X-RAY DIFFRACTIONf_dihedral_angle_d15.351993
X-RAY DIFFRACTIONf_chiral_restr0.057366
X-RAY DIFFRACTIONf_plane_restr0.003465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8812-1.92830.21931500.21462593X-RAY DIFFRACTION94
1.9283-1.98040.21300.19582661X-RAY DIFFRACTION95
1.9804-2.03870.18811470.17692584X-RAY DIFFRACTION95
2.0387-2.10450.16951500.16252627X-RAY DIFFRACTION95
2.1045-2.17970.15851380.15142593X-RAY DIFFRACTION95
2.1797-2.26690.15131210.14362666X-RAY DIFFRACTION96
2.2669-2.370.17761190.14082634X-RAY DIFFRACTION96
2.37-2.49490.13731380.13882646X-RAY DIFFRACTION95
2.4949-2.65120.15971160.14032621X-RAY DIFFRACTION96
2.6512-2.85570.16071340.14032643X-RAY DIFFRACTION95
2.8557-3.14280.15411540.13732590X-RAY DIFFRACTION94
3.1428-3.5970.181320.13722636X-RAY DIFFRACTION95
3.597-4.52940.13691440.11392617X-RAY DIFFRACTION95
4.5294-30.30940.18461650.14932598X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8188-0.04250.6860.5102-0.72095.4765-0.0602-0.19910.113-0.0082-0.02030.00090.0678-0.24120.01010.1047-0.03320.00820.1194-0.01690.1196-9.6243-1.61824.2804
21.498-0.0242-0.82841.65120.43288.1347-0.0704-0.1289-0.0498-0.1026-0.0348-0.05230.09180.17970.04950.0377-0.0290.00640.09980.00090.1658-11.2242-12.4210.9973
30.8040.106-0.37811.0093-1.15175.7824-0.0225-0.0487-0.0606-0.13580.01110.00040.0464-0.1079-0.02870.0741-0.0221-0.0040.1045-0.01070.1075-5.2416-7.335-5.0377
41.58360.1398-0.61821.40530.87656.1217-0.1330.01040.0727-0.12590.17640.0197-0.1521-0.0125-0.05570.0781-0.0267-0.00050.08230.02250.1412-15.7961-4.7164-6.1811
50.4058-0.0929-0.37421.10942.14089.4855-0.0542-0.0416-0.0137-0.0692-0.02750.0924-0.0899-0.10460.09920.0536-0.017-0.0010.11370.00450.122-33.4485-14.5999-0.5086
61.26880.20120.53880.85090.21173.4772-0.14390.070.0117-0.16980.0942-0.00620.1658-0.03960.01310.0966-0.04320.00010.09690.00430.1401-23.5794-18.802-6.2787
70.9398-0.1212-1.32960.70170.55144.9595-0.0768-0.1253-0.04570.00790.0591-0.0537-0.08540.2095-0.02190.0795-0.0237-0.00680.10040.00290.1248-29.7125-21.45043.9191
81.01850.2939-0.22131.4436-0.18813.05710.0363-0.29080.0619-0.0748-0.09320.0289-0.0437-0.12890.00190.0504-0.02310.02150.1728-0.00920.1215-26.5186-11.08315.4816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 84 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 47 )
4X-RAY DIFFRACTION4chain 'B' and (resid 48 through 84 )
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 42 )
6X-RAY DIFFRACTION6chain 'C' and (resid 43 through 85 )
7X-RAY DIFFRACTION7chain 'D' and (resid 5 through 47 )
8X-RAY DIFFRACTION8chain 'D' and (resid 48 through 84 )

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