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- PDB-4gzr: Crystal structure of the Mycobacterium tuberculosis H37Rv EsxOP (... -

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Basic information

Entry
Database: PDB / ID: 4gzr
TitleCrystal structure of the Mycobacterium tuberculosis H37Rv EsxOP (Rv2346c-Rv2347c) complex in space group C2221
Components
  • ESAT-6-like protein 6
  • ESAT-6-like protein 7
KeywordsStructural Genomics / Unknown Function / WXG100 / TB Structural Genomics Consortium / TBSGC / Integrated Center for Structure and Function Innovation / ISFI / Secreted / PSI-2 / Protein Structure Initiative
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.553 Å
AuthorsArbing, M.A. / Chan, S. / He, Q. / Harris, L. / Zhou, T.T. / Kuo, E. / Ahn, C.J. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC) / Integrated Center for Structure and Function Innovation (ISFI)
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
DepositionSep 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Other
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Sep 13, 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: ESAT-6-like protein 6
B: ESAT-6-like protein 7
C: ESAT-6-like protein 6
D: ESAT-6-like protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0295
Polymers43,9324
Non-polymers961
Water55831
1
A: ESAT-6-like protein 6
B: ESAT-6-like protein 7


Theoretical massNumber of molelcules
Total (without water)21,9662
Polymers21,9662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-23 kcal/mol
Surface area8130 Å2
MethodPISA
2
C: ESAT-6-like protein 6
D: ESAT-6-like protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0623
Polymers21,9662
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-29 kcal/mol
Surface area8460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.100, 112.070, 95.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsDimeric assembly 1 is composed of chains A and B. / Dimeric assembly 2 is composed of chains C and D.

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Components

#1: Protein ESAT-6-like protein 6


Mass: 10890.939 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 ESAT-6-like protein 7 / CFP-10 homologue


Mass: 11075.280 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: Reservoir: 11% PEG3350, 40 mM Citric Acid pH 3.5. Protein concentration: 7.8 mg/mL. Protein Buffer: 20 mM HEPES, pH 7.8, 150 mM NaCl, 2 mM ZnSO4, 38 mM B-ME., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.282 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2012
RadiationMonochromator: CRYO-COOLED SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.55→52.531 Å / Num. all: 13597 / Num. obs: 13340 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.56 % / Biso Wilson estimate: 74.899 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.55-2.620.6752.725125946195.3
2.62-2.690.6553.255405955199.5
2.69-2.770.5084.125095929198.7
2.77-2.850.4184.934637902198.7
2.85-2.950.3037.225131885199.4
2.95-3.050.2169.275009845199.5
3.05-3.170.17711.274789827199.6
3.17-3.30.13913.414532786199.5
3.3-3.440.10715.924364771199.1
3.44-3.610.08918.563847720198.6
3.61-3.810.0721.693661695198.7
3.81-4.040.06224.043794655199.1
4.04-4.310.05925.683538623198.3
4.31-4.660.0527.483194565197.8
4.66-5.110.05227.562892533196.6
5.11-5.710.05326.122389464195.3
5.71-6.590.05227.482448428196.8
6.59-8.070.04629.22038362196
8.07-11.420.03929.911441282192.5
11.42-52.5310.04230.99885167191.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å62.96 Å
Translation2.5 Å62.96 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.4.0phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OGI

3ogi


Resolution: 2.553→38.05 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.8083 / SU ML: 0.27 / σ(F): 1.99 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 1332 10 %Random
Rwork0.1987 ---
obs0.202 13314 97.95 %-
all-13597 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.77 Å2 / Biso mean: 43.4823 Å2 / Biso min: 14.63 Å2
Refinement stepCycle: LAST / Resolution: 2.553→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 5 31 2196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142208
X-RAY DIFFRACTIONf_angle_d1.2252974
X-RAY DIFFRACTIONf_chiral_restr0.07311
X-RAY DIFFRACTIONf_plane_restr0.005406
X-RAY DIFFRACTIONf_dihedral_angle_d17.001798
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5526-2.64380.28581280.25161161128996
2.6438-2.74960.27111310.25421174130599
2.7496-2.87470.29661300.22721181131198
2.8747-3.02620.28741350.221912141349100
3.0262-3.21570.29161340.21421203133799
3.2157-3.46380.2271340.20961198133299
3.4638-3.81210.24351340.17871205133998
3.8121-4.36310.18471340.17581202133699
4.3631-5.49440.19211330.18591201133496
5.4944-38.05420.2531390.20291243138295
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)
12.86512.9206-0.7228.1407-1.13253.41640.0935-0.4276-0.35580.2888-0.2223-0.90660.47850.24090.09270.34430.006-0.08030.1768-0.09660.236118.5228-17.3555-9.1469
23.38281.4534-0.01893.1493-0.28251.7034-0.2730.4531-0.4316-0.19250.4522-0.12670.72010.0305-0.13550.4018-0.17250.07210.2906-0.10450.29936.603-20.3333-15.9125
32.45541.2147-0.26585.09861.03972.44110.1117-0.0333-0.08820.2245-0.12140.65510.2774-0.3879-0.00160.2436-0.03480.00560.20230.07650.24869.29724.6038-7.8778
42.8320.6035-0.19612.7457-0.08612.51990.0707-0.1203-0.0391-0.09930.1323-0.3301-0.16260.2191-0.20530.2426-0.0930.01360.18-0.03970.342718.91718.3423-16.2301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 12:69)A12 - 69
2X-RAY DIFFRACTION2(chain B and resid 4:95)B4 - 95
3X-RAY DIFFRACTION3(chain C and resid 9:69)C9 - 69
4X-RAY DIFFRACTION4(chain D and resid 3:94)D3 - 94

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