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- PDB-4iyi: The crystal structure of a secreted protein EsxB (wild-type, C-te... -

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Basic information

Entry
Database: PDB / ID: 4iyi
TitleThe crystal structure of a secreted protein EsxB (wild-type, 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 / ESAT-6-like protein / ESAT-6-like protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.083 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, 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 1.1Sep 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
C: Secreted protein EsxB
D: Secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,77922
Polymers44,2294
Non-polymers1,55018
Water2,360131
1
A: Secreted protein EsxB
B: Secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,81210
Polymers22,1152
Non-polymers6978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-122 kcal/mol
Surface area8500 Å2
MethodPISA
2
C: Secreted protein EsxB
D: Secreted protein EsxB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,96712
Polymers22,1152
Non-polymers85310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-137 kcal/mol
Surface area8670 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17870 Å2
ΔGint-278 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.211, 77.211, 71.092
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Secreted protein EsxB


Mass: 11057.279 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
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.77 Å3/Da / Density % sol: 55.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium Acetate, 2.0M Ammonium Sulfate, pH 4.5, 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 315r / Detector: CCD / Date: Oct 15, 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
Reflection twinOperator: -h,-k,l / Fraction: 0.49
ReflectionResolution: 2.08→39 Å / Num. all: 28219 / Num. obs: 28219 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 18.2
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1392 / % possible all: 100

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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: 4IYH

4iyh


Resolution: 2.083→38.605 Å / σ(F): 1.96 / Phase error: 16.27 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1668 1430 5.07 %random
Rwork0.1534 ---
obs0.155 28197 99.49 %-
all-28197 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.083→38.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 85 131 2722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072605
X-RAY DIFFRACTIONf_angle_d0.8753491
X-RAY DIFFRACTIONf_dihedral_angle_d15.987974
X-RAY DIFFRACTIONf_chiral_restr0.057360
X-RAY DIFFRACTIONf_plane_restr0.003461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0856-2.16020.21571360.17982698X-RAY DIFFRACTION95
2.1602-2.24660.20491550.17352666X-RAY DIFFRACTION95
2.2466-2.34890.19951470.16832679X-RAY DIFFRACTION95
2.3489-2.47270.20711180.16252687X-RAY DIFFRACTION96
2.4727-2.62750.1661590.16952663X-RAY DIFFRACTION94
2.6275-2.83030.17161290.15912719X-RAY DIFFRACTION95
2.8303-3.1150.15381430.14552657X-RAY DIFFRACTION95
3.115-3.56530.16191410.14562673X-RAY DIFFRACTION95
3.5653-4.49020.14311360.12862668X-RAY DIFFRACTION94
4.4902-33.93050.17691620.16332621X-RAY DIFFRACTION93
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)
11.321-0.14981.25410.8512-1.04752.3732-0.1614-0.0860.2173-0.0376-0.12540.0127-0.01280.07610.2850.112-0.0274-0.00690.10740.01190.2636-9.2573-0.7306-0.5843
21.76460.4801-0.34451.1072-0.21452.1044-0.1255-0.2365-0.092-0.0013-0.12330.07490.277-0.10020.19630.0425-0.0233-0.00170.11190.00860.3076-10.7606-11.28866.3498
30.8108-0.28860.03731.7188-2.40025.7509-0.1487-0.0435-0.0453-0.1254-0.0709-0.07290.1474-0.02840.22690.068-0.0435-0.01210.0884-0.00230.2346-4.9663-7.4673-3.9194
41.9624-0.0937-1.01691.74870.43863.5919-0.2518-0.0214-0.103-0.21960.13360.138-0.1407-0.01180.10450.1242-0.05170.01420.06680.00610.2751-15.584-4.9007-7.1494
50.4710.15320.41181.79342.96725.4804-0.3342-0.03150.0678-0.0506-0.26010.306-0.0437-0.22470.47420.0583-0.02050.01830.159-0.02030.2699-33.2545-13.87671.6008
62.37730.52881.14191.51760.58824.1963-0.18230.0722-0.0877-0.22580.049-0.0950.12290.15560.11080.0638-0.02920.02930.0459-0.00940.2665-24.1558-19.1587-7.9281
71.2693-0.6259-2.36341.08111.41166.8313-0.241-0.1757-0.1445-0.0013-0.1178-0.0073-0.08160.28530.3050.0528-0.044-0.01250.1375-0.02940.2803-29.5817-21.51253.9172
82.22320.3970.8611.454-0.1286.6744-0.0044-0.29580.1361-0.1044-0.0264-0.123-0.2928-0.0859-0.01210.0512-0.01680.03340.12570.02330.3032-26.0904-11.24746.2057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 84 )
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 45 )
4X-RAY DIFFRACTION4chain 'B' and (resid 46 through 84 )
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 39 )
6X-RAY DIFFRACTION6chain 'C' and (resid 40 through 85 )
7X-RAY DIFFRACTION7chain 'D' and (resid 5 through 47 )
8X-RAY DIFFRACTION8chain 'D' and (resid 48 through 83 )

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