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- PDB-4j10: The crystal structure of a secreted protein ESXB (SeMet-labeled) ... -

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Basic information

Entry
Database: PDB / ID: 4j10
TitleThe crystal structure of a secreted protein ESXB (SeMet-labeled) 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
FORMIC ACID / ESAT-6-like protein / ESAT-6-like protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 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 (Semet-Labeled) 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: 4IOE
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0715
Polymers20,9332
Non-polymers1383
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-27 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.080, 38.394, 130.765
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: 10466.316 Da / Num. of mol.: 2
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-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M PHOSPHATE-CITRATE, 40% PEG300, 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: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / 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: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.44→28.9 Å / Num. all: 30476 / Num. obs: 30476 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 46.1
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1285 / % possible all: 85.2

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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: 1.44→28.81 Å / SU ML: 0.06 / σ(F): 1.34 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1542 5.08 %random
Rwork0.179 ---
obs0.18 30371 97.8 %-
all-30371 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 9 149 1497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061444
X-RAY DIFFRACTIONf_angle_d0.9761947
X-RAY DIFFRACTIONf_dihedral_angle_d16.039572
X-RAY DIFFRACTIONf_chiral_restr0.063208
X-RAY DIFFRACTIONf_plane_restr0.004265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4401-1.48660.25251110.21192306X-RAY DIFFRACTION88
1.4866-1.53970.19981450.1872580X-RAY DIFFRACTION98
1.5397-1.60140.20261410.16292600X-RAY DIFFRACTION99
1.6014-1.67420.1691440.16382627X-RAY DIFFRACTION99
1.6742-1.76250.22641480.16922623X-RAY DIFFRACTION100
1.7625-1.87290.20241410.1642660X-RAY DIFFRACTION100
1.8729-2.01750.21491440.17272657X-RAY DIFFRACTION100
2.0175-2.22040.19881180.16662700X-RAY DIFFRACTION100
2.2204-2.54160.20091540.16992688X-RAY DIFFRACTION100
2.5416-3.20140.21471430.18392715X-RAY DIFFRACTION100
3.2014-28.81680.1981530.19082673X-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)
14.9255-0.22591.69571.8630.52144.7942-0.0864-0.09090.66970.2746-0.039-0.1908-0.21380.24810.10190.29130.0104-0.0290.1747-0.00890.25964.466529.645743.9583
21.6553-2.1337-0.61752.85710.33672.16470.02120.0323-0.07010.265-0.02980.19670.1017-0.378-0.01290.1939-0.0139-0.00220.1203-0.00540.1592-0.815722.099733.7534
32.13880.38811.03951.0438-1.12992.22990.05050.2534-0.0799-0.14490.16440.08850.4078-0.2875-0.17690.1652-0.0278-0.00730.17360.00130.1671-3.778318.391510.9291
41.72940.43221.36331.9038-0.84532.33510.03460.3254-0.2133-0.46620.0188-0.05590.62260.0575-0.02160.37140.02470.03860.2562-0.03240.20892.757713.70541.3897
51.1292-0.06-1.26890.94231.04432.3951-0.0151-0.0031-0.0840.1081-0.0586-0.03560.5728-0.09160.04830.21780.0048-0.0160.11380.01210.16632.846814.035430.5982
64.66222.21861.81743.4133-1.53533.16220.3064-1.05171.50851.1609-0.28480.1988-1.4350.1030.14880.5843-0.1091-0.02140.3374-0.0810.3187-1.197117.060251.1677
70.9235-0.41550.06781.2454-1.46152.925-0.08080.05790.13150.0626-0.0649-0.1011-0.24690.10.12610.09750.00360.00420.1460.01270.16863.953226.103516.0982
81.3377-0.31891.60791.1406-1.09948.0643-0.03490.1972-0.00310.0064-0.1044-0.18690.12880.68690.15680.07550.01170.00060.21330.02060.19829.713921.258413.5048
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 40 )
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 60 )
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 88 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 85 )

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