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- PDB-3ogi: Crystal structure of the Mycobacterium tuberculosis H37Rv EsxOP c... -

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Basic information

Entry
Database: PDB / ID: 3ogi
TitleCrystal structure of the Mycobacterium tuberculosis H37Rv EsxOP complex (Rv2346c-Rv2347c)
Components
  • Putative ESAT-6-like protein 6
  • Putative ESAT-6-like protein 7
KeywordsStructural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI / TB Structural Genomics Consortium / TBSGC / WXG100 / Secreted
Function / homology
Function and homology information


cell wall / peptidoglycan-based cell wall / extracellular region / plasma membrane
Similarity search - Function
ESAT-6-like protein, Mycobacterium / ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ESAT-6-like protein EsxO / ESAT-6-like protein EsxP / ESAT-6-like protein EsxP / ESAT-6-like protein EsxO
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.549 Å
AuthorsArbing, M.A. / Chan, S. / Zhou, T.T. / Ahn, C. / Harris, L. / Kuo, E. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. / Integrated Center for Structure and Function Innovation (ISFI) / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Plos One / Year: 2013
Title: Heterologous expression of mycobacterial Esx complexes in Escherichia coli for structural studies is facilitated by the use of maltose binding protein fusions.
Authors: Arbing, M.A. / Chan, S. / Harris, L. / Kuo, E. / Zhou, T.T. / Ahn, C.J. / Nguyen, L. / He, Q. / Lu, J. / Menchavez, P.T. / Shin, A. / Holton, T. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 21, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ESAT-6-like protein 6
B: Putative ESAT-6-like protein 7
C: Putative ESAT-6-like protein 6
D: Putative ESAT-6-like protein 7


Theoretical massNumber of molelcules
Total (without water)45,0584
Polymers45,0584
Non-polymers00
Water63135
1
A: Putative ESAT-6-like protein 6
B: Putative ESAT-6-like protein 7


Theoretical massNumber of molelcules
Total (without water)22,5292
Polymers22,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-21 kcal/mol
Surface area9240 Å2
MethodPISA
2
C: Putative ESAT-6-like protein 6
D: Putative ESAT-6-like protein 7


Theoretical massNumber of molelcules
Total (without water)22,5292
Polymers22,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-21 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.383, 66.383, 162.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative ESAT-6-like protein 6 / EsxP


Mass: 11031.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2411, MTCY98.15c, Rv2346c / Plasmid: pMAPLe3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95242, UniProt: P9WNI7*PLUS
#2: Protein Putative ESAT-6-like protein 7 / EsxO


Mass: 11497.335 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT2412, MTCY98.16c, Rv2347c / Plasmid: pMAPLe3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95243, UniProt: P9WNI5*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Reservoir: 9.0% isopropanol, 200 mM CaCl2, 90 mM sodium acetate trihydrate pH 4.6. Protein buffer: 50 mM HEPES pH 7.8, 150 mM NaCl. Ratio = 2:1 protein solution to reservoir solution, VAPOR ...Details: Reservoir: 9.0% isopropanol, 200 mM CaCl2, 90 mM sodium acetate trihydrate pH 4.6. Protein buffer: 50 mM HEPES pH 7.8, 150 mM NaCl. Ratio = 2:1 protein solution to reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918, 0.97938
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2010
RadiationMonochromator: CRYO-COOLED SI(111) DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.979381
ReflectionResolution: 2.55→100 Å / Num. obs: 25291 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 55.54 Å2 / Rmerge(I) obs: 0.078
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.4 / % possible all: 96.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.549→28.307 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.26 666 4.86 %Random
Rwork0.216 ---
obs0.2181 13697 96.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.073 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å2-0 Å2
2--0.64 Å2-0 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.549→28.307 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 0 35 2117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082125
X-RAY DIFFRACTIONf_angle_d1.0672857
X-RAY DIFFRACTIONf_dihedral_angle_d15.987783
X-RAY DIFFRACTIONf_chiral_restr0.072305
X-RAY DIFFRACTIONf_plane_restr0.003390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5494-2.74610.31491380.27682492X-RAY DIFFRACTION95
2.7461-3.02220.31661260.23682607X-RAY DIFFRACTION98
3.0222-3.45880.24111280.2112649X-RAY DIFFRACTION99
3.4588-4.35520.25161310.19312653X-RAY DIFFRACTION98
4.3552-28.30830.25081430.21992630X-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)
10.7040.0999-0.41650.6128-0.1880.3407-0.1619-0.1955-0.0924-0.03720.13950.1003-0.0019-0.0709-0.04550.30480.18530.00510.48550.02980.2665-14.43483.610570.3348
21.7202-0.5503-0.73622.8645-0.51880.5322-0.2213-0.13040.0271-0.38760.38440.1068-0.0132-0.2153-0.12050.41170.2-0.08490.4044-0.0160.2662-11.716914.530463.0197
30.4950.4362-0.02480.82760.19991.3459-0.1493-0.1520.0919-0.15550.19840.0546-0.08890.3394-0.05580.39730.13270.01720.4599-0.08630.32777.59731.829774.6162
43.22-1.3213-0.42393.8855-0.50241.247-0.1403-0.0468-0.2199-0.68010.2106-0.07680.11990.1993-0.0210.37350.16060.01640.3073-0.02560.19517.0602-8.429964.8124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 13:69)
2X-RAY DIFFRACTION2(chain B and resid 5:97)
3X-RAY DIFFRACTION3(chain C and resid 13:68)
4X-RAY DIFFRACTION4(chain D and resid 7:97)

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