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- PDB-4j11: The crystal structure of a secreted protein ESXB (wild-type, in P... -

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Basic information

Entry
Database: PDB / ID: 4j11
TitleThe crystal structure of a secreted protein ESXB (wild-type, in P21 space group) 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: 1.44 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 (Wild-Type, in P21 Space Group) from Bacillus Anthracis Str. Sterne
Authors: Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionJan 31, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 13, 2013ID: 4IOG
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)41,4904
Polymers41,4904
Non-polymers00
Water8,593477
1
A: SECRETED PROTEIN ESXB
B: SECRETED PROTEIN ESXB


Theoretical massNumber of molelcules
Total (without water)20,7452
Polymers20,7452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-27 kcal/mol
Surface area10070 Å2
MethodPISA
2
C: SECRETED PROTEIN ESXB
D: SECRETED PROTEIN ESXB


Theoretical massNumber of molelcules
Total (without water)20,7452
Polymers20,7452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-27 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.686, 132.846, 38.675
Angle α, β, γ (deg.)90.00, 98.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SECRETED PROTEIN ESXB


Mass: 10372.526 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, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 1.94 Å3/Da / Density % sol: 36.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M SODIUM CHLORIDE, 0.1M TRIS:HCL, 30% (W/V) PEG3000, PH 7.0, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2011 / Details: MIRROR
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.44→31.3 Å / Num. all: 55739 / Num. obs: 55739 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 35.2
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2344 / % possible all: 85

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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: 4IOE

4ioe
PDB Unreleased entry


Resolution: 1.44→31.3 Å / SU ML: 0.13 / σ(F): 1.38 / Phase error: 20.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 2818 5.06 %
Rwork0.169 --
obs0.17 55667 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 0 477 3279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063001
X-RAY DIFFRACTIONf_angle_d0.9824051
X-RAY DIFFRACTIONf_dihedral_angle_d15.8181191
X-RAY DIFFRACTIONf_chiral_restr0.066427
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4378-1.46260.26571110.20561862X-RAY DIFFRACTION71
1.4626-1.48920.20261160.18982604X-RAY DIFFRACTION94
1.4892-1.51780.23751520.18472644X-RAY DIFFRACTION99
1.5178-1.54880.20131420.17792699X-RAY DIFFRACTION99
1.5488-1.58250.23131330.16572728X-RAY DIFFRACTION100
1.5825-1.61930.19621350.16192679X-RAY DIFFRACTION100
1.6193-1.65980.2111210.16562733X-RAY DIFFRACTION100
1.6598-1.70470.23291560.17172679X-RAY DIFFRACTION100
1.7047-1.75480.25431370.17772740X-RAY DIFFRACTION100
1.7548-1.81140.18551440.17782650X-RAY DIFFRACTION100
1.8114-1.87620.21161480.17112753X-RAY DIFFRACTION100
1.8762-1.95130.21460.1732677X-RAY DIFFRACTION100
1.9513-2.04010.19851560.17242721X-RAY DIFFRACTION100
2.0401-2.14760.1711310.15692732X-RAY DIFFRACTION100
2.1476-2.28210.17361420.15482698X-RAY DIFFRACTION100
2.2821-2.45830.19571630.15792703X-RAY DIFFRACTION100
2.4583-2.70550.18681420.16832709X-RAY DIFFRACTION100
2.7055-3.09670.20791540.17272692X-RAY DIFFRACTION99
3.0967-3.90040.1841480.15752635X-RAY DIFFRACTION96
3.9004-31.35240.20841410.18342511X-RAY DIFFRACTION92
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)
14.5221-0.9274-2.99884.2060.75598.95680.083-0.1959-0.0330.19240.12540.67310.0232-0.6668-0.18190.11260.00970.00930.18220.00090.1546-2.528226.584332.1361
20.0310.8610.34448.02941.22720.3706-0.0020.0115-0.0333-0.0380.0564-0.346-0.00580.0359-0.06340.0662-0.00550.02610.0929-0.01170.09784.7987-1.199619.8501
30.4811.70520.37814.67330.8918-0.0043-0.06210.00260.0073-0.6420.0552-0.0896-0.03540.0056-0.00110.1815-0.01830.00460.0893-0.00080.09511.16854.483213.1578
40.2096-0.38880.18266.2613-0.74810.26450.00960.0184-0.05160.04010.01830.2933-0.0357-0.032-0.02220.0337-0.00260.00390.08870.00020.0707-2.5395-5.942624.2734
50.2806-0.22260.17318.2493-1.4250.51860.0006-0.0191-0.023-0.15980.06230.58890.0147-0.0428-0.08220.0574-0.0029-0.01980.1042-0.00440.1205-7.6996-6.633319.8949
60.42780.4664-0.22571.6167-0.05231.2435-0.0475-0.0157-0.04560.1130.06760.1340.2131-0.0677-0.01460.053-0.0112-0.00220.09290.00610.06247.462423.39722.6626
70.80731.3297-0.01798.27760.07840.7845-0.02760.0524-0.0725-0.25450.0625-0.09390.19410.0134-0.03380.09190.00220.00630.1082-0.00770.037211.565420.4621-4.9414
80.81770.14160.05391.98431.02851.0324-0.0415-0.0430.08510.07530.0861-0.0959-0.0319-0.0438-0.03560.02230.0057-0.00480.1248-0.00890.06612.4435.81366.27
90.8624-0.1225-0.12065.95831.13041.1462-0.04290.022-0.07650.34280.1312-0.56570.1980.0917-0.06690.0380.0211-0.02780.149-0.01630.11419.600829.39832.9033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 7 )
2X-RAY DIFFRACTION2chain 'A' and (resid 8 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 85 )
4X-RAY DIFFRACTION4chain 'B' and (resid -2 through 44 )
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 90 )
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 44 )
7X-RAY DIFFRACTION7chain 'C' and (resid 45 through 90 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 39 )
9X-RAY DIFFRACTION9chain 'D' and (resid 40 through 86 )

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