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- PDB-4j7j: The crystal structure of a secreted protein EsxB (Mutant G53A) fr... -

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Basic information

Entry
Database: PDB / ID: 4j7j
TitleThe crystal structure of a secreted protein EsxB (Mutant G53A) from Bacillus anthracis str. Sterne
Componentssecreted protein EsxB
KeywordsUNKNOWN FUNCTION / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyHP0062-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 / ESAT-6-like protein / ESAT-6-like protein
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.458 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 (Mutant, G53A) from Bacillus anthracis str. Sterne
Authors: Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionFeb 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8653
Polymers20,7732
Non-polymers921
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-28 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.064, 38.445, 130.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein secreted protein EsxB


Mass: 10386.552 Da / Num. of mol.: 2 / Mutation: G53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: Bacillus anthracis, BAS2036, BA_2191, GBAA_2191 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81R67, UniProt: A0A6L7HJC4*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.39 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium Acetate:HCl, 25% (w/v) PEG3350 , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2011 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.46→30 Å / Num. all: 29127 / Num. obs: 29127 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 36.1
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 4 / Num. unique all: 1222 / % possible all: 82.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4J11

4j11


Resolution: 1.458→29.494 Å / SU ML: 0.13 / σ(F): 1.35 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 1471 5.07 %Random
Rwork0.1824 ---
obs0.1841 29023 96.79 %-
all-29023 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.458→29.494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 6 199 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061410
X-RAY DIFFRACTIONf_angle_d0.9821892
X-RAY DIFFRACTIONf_dihedral_angle_d15.756549
X-RAY DIFFRACTIONf_chiral_restr0.065203
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4576-1.50460.27851130.23252142X-RAY DIFFRACTION84
1.5046-1.55840.26091260.20382375X-RAY DIFFRACTION94
1.5584-1.62080.26911340.17782526X-RAY DIFFRACTION99
1.6208-1.69460.21881420.17152528X-RAY DIFFRACTION100
1.6946-1.78390.19641280.17662548X-RAY DIFFRACTION100
1.7839-1.89560.23231140.17372578X-RAY DIFFRACTION100
1.8956-2.0420.23971300.18832584X-RAY DIFFRACTION99
2.042-2.24740.24291210.17592561X-RAY DIFFRACTION99
2.2474-2.57240.20791670.17822531X-RAY DIFFRACTION99
2.5724-3.24040.22041600.18632572X-RAY DIFFRACTION98
3.2404-29.49970.1881360.18082607X-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)
10.6661-0.1135-0.01491.3626-0.26894.4059-0.05350.06380.0289-0.0257-0.00990.01330.1708-0.15690.0660.0756-0.00320.00420.07920.00690.1413-1.24342.358722.2775
20.7482-0.0606-0.29651.60110.38947.73910.05170.0224-0.043-0.1289-0.0701-0.11870.469-0.04320.0110.15290.01030.00430.07270.00480.14792.734-5.104523.5118
31.998-0.3581-0.8740.30820.62481.27380.04610.7894-0.6439-0.1835-0.23480.06280.5407-0.31560.17830.4907-0.0273-0.03650.5131-0.0920.2634-3.51980.139-13.2539
41.3594-0.19861.3220.7823-0.82398.6229-0.07090.03810.12670.082-0.0826-0.1211-0.22850.19380.18780.1028-0.0064-0.01570.11680.0080.16615.00827.16919.4048
51.8492-0.30731.45561.0414-0.98257.6121-0.0190.25060.0693-0.0642-0.1692-0.18590.23460.76460.21250.0820.0280.00160.17910.01690.17469.66091.694513.8202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 90 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 7 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 44 )
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 85 )

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