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- PDB-4j42: The crystal structure of a secreted protein EsxB (Mutant Y65F) fr... -

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Basic information

Entry
Database: PDB / ID: 4j42
TitleThe crystal structure of a secreted protein EsxB (Mutant Y65F) 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
CITRATE ANION / FORMIC ACID / ESAT-6-like protein / ESAT-6-like protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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 Y65F) from Bacillus anthracis str. Sterne
Authors: Fan, Y. / Tan, K. / Chhor, G. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionFeb 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 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)21,0406
Polymers20,7132
Non-polymers3274
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-53 kcal/mol
Surface area8730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.221, 76.221, 71.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein secreted protein EsxB


Mass: 10356.526 Da / Num. of mol.: 2 / Mutation: Y65F
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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris propane, 2M di-ammonium hydrogen citrate, pH 7.0, 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: 0.97921 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: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.28→34 Å / Num. all: 61931 / Num. obs: 61931 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 40.7
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3054 / % possible all: 99.9

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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 4IYI

4iyi


Resolution: 1.28→33.619 Å / SU ML: 0.1 / σ(F): 1.35 / Phase error: 16.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 3139 5.07 %random
Rwork0.1625 ---
obs0.1631 61898 99.8 %-
all-61898 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.28→33.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1287 0 22 139 1448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051358
X-RAY DIFFRACTIONf_angle_d0.9691823
X-RAY DIFFRACTIONf_dihedral_angle_d13.815530
X-RAY DIFFRACTIONf_chiral_restr0.063193
X-RAY DIFFRACTIONf_plane_restr0.004248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.30.24961290.25462633X-RAY DIFFRACTION100
1.3-1.32130.2181380.21762686X-RAY DIFFRACTION100
1.3213-1.34410.23611540.1972600X-RAY DIFFRACTION100
1.3441-1.36850.23461230.19222664X-RAY DIFFRACTION100
1.3685-1.39490.17981350.18672654X-RAY DIFFRACTION100
1.3949-1.42330.17571410.17782637X-RAY DIFFRACTION100
1.4233-1.45430.19091520.17392661X-RAY DIFFRACTION100
1.4543-1.48810.18261360.1682667X-RAY DIFFRACTION100
1.4881-1.52530.18181400.15262656X-RAY DIFFRACTION100
1.5253-1.56660.17171410.15382632X-RAY DIFFRACTION100
1.5666-1.61270.17351370.15192693X-RAY DIFFRACTION100
1.6127-1.66470.1541520.1522643X-RAY DIFFRACTION100
1.6647-1.72420.18111460.15572635X-RAY DIFFRACTION100
1.7242-1.79330.16311360.16082675X-RAY DIFFRACTION100
1.7933-1.87490.16651480.15552684X-RAY DIFFRACTION100
1.8749-1.97370.17191410.1592683X-RAY DIFFRACTION100
1.9737-2.09730.15131500.152680X-RAY DIFFRACTION100
2.0973-2.25920.15971450.14792666X-RAY DIFFRACTION100
2.2592-2.48650.17811510.15862707X-RAY DIFFRACTION100
2.4865-2.84620.17271470.16072713X-RAY DIFFRACTION100
2.8462-3.58520.17481440.15562736X-RAY DIFFRACTION100
3.5852-33.63040.17131530.17112754X-RAY DIFFRACTION97
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)
10.45310.1420.44710.3153-0.18725.29230.0321-0.040.00470.0363-0.03040.0467-0.13570.0072-0.00040.14850.0308-0.00040.0666-0.0070.1308-41.483513.6877-10.1674
21.0922-0.0941-0.03431.61370.53062.09710.0639-0.00010.03340.083-0.0343-0.0546-0.09190.131-0.05150.0849-0.0147-0.00040.02770.00360.1163-33.58477.3207-7.6235
30.8310.00910.82541.1938-0.71963.89230.04120.05720.01470.0125-0.1004-0.05370.06860.12720.07640.09030.00830.00820.0502-0.00110.1101-34.274614.1743-16.9835
41.0006-0.00660.38291.9233-0.10584.90450.0577-0.04120.0635-0.0023-0.0390.0592-0.2075-0.4591-0.04760.09080.0333-0.00870.0504-0.00160.1218-42.57256.5037-14.0218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 84 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 47 )
4X-RAY DIFFRACTION4chain 'B' and (resid 48 through 89 )

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