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- PDB-3fav: Structure of the CFP10-ESAT6 complex from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 3fav
TitleStructure of the CFP10-ESAT6 complex from Mycobacterium tuberculosis
Components
  • 6 kDa early secretory antigenic target
  • ESAT-6-like protein esxB
KeywordsVIRAL PROTEIN / Complex / Operon structure / Four-helical-bundle / Coiled-coil / WXG-motif / Mycobacterium tuberculosis / secreted / secretion system / adaptor protein / proposed virulent factor
Function / homology
Function and homology information


symbiont-mediated suppression of host T-cell mediated immune response / protein secretion by the type VII secretion system / symbiont-mediated perturbation of host signal transduction pathway / Manipulation of host energy metabolism / : / host cell surface binding / host cell endoplasmic reticulum / host cell membrane / membrane => GO:0016020 / peptidoglycan-based cell wall ...symbiont-mediated suppression of host T-cell mediated immune response / protein secretion by the type VII secretion system / symbiont-mediated perturbation of host signal transduction pathway / Manipulation of host energy metabolism / : / host cell surface binding / host cell endoplasmic reticulum / host cell membrane / membrane => GO:0016020 / peptidoglycan-based cell wall / Modulation by Mtb of host immune system / host cell surface / host cell plasma membrane / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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
IMIDAZOLE / 6 kDa early secretory antigenic target / ESAT-6-like protein EsxB / ESAT-6-like protein EsxB / 6 kDa early secretory antigenic target
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPoulsen, C. / Holton, S.J. / Wilmanns, M. / Song, Y.H.
CitationJournal: Plos One / Year: 2014
Title: WXG100 protein superfamily consists of three subfamilies and exhibits an alpha-helical C-terminal conserved residue pattern.
Authors: Poulsen, C. / Panjikar, S. / Holton, S.J. / Wilmanns, M. / Song, Y.H.
History
DepositionNov 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 esxB
B: 6 kDa early secretory antigenic target
C: ESAT-6-like protein esxB
D: 6 kDa early secretory antigenic target
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,83012
Polymers41,3034
Non-polymers5278
Water5,549308
1
A: ESAT-6-like protein esxB
B: 6 kDa early secretory antigenic target
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9827
Polymers20,6512
Non-polymers3315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-82 kcal/mol
Surface area7530 Å2
MethodPISA
2
C: ESAT-6-like protein esxB
D: 6 kDa early secretory antigenic target
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8485
Polymers20,6512
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-87 kcal/mol
Surface area8840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.340, 23.930, 83.860
Angle α, β, γ (deg.)90.000, 94.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-96-

ZN

21B-215-

HOH

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Components

#1: Protein ESAT-6-like protein esxB / CFP-10 / 10 kDa culture filtrate antigen cfp10 / Secreted antigenic protein MTSA-10


Mass: 10873.819 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct contained the entire protein encoding region of the CFP10-ESAT6 operon including its intergenic region
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxB / Plasmid details: modified pSD26 vector / Plasmid: pMyNT / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): MC2 155 / References: UniProt: P0A566, UniProt: P9WNK5*PLUS
#2: Protein 6 kDa early secretory antigenic target / ESAT-6


Mass: 9777.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The construct contained the entire protein encoding region of the CFP10-ESAT6 operon including its intergenic region
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: esxA / Plasmid details: modified pSD26 vector / Plasmid: pMyNT / Production host: Mycobacterium smegmatis (bacteria) / Strain (production host): MC2 155 / References: UniProt: P0A564, UniProt: P9WNK7*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 33% (v/v) PEG 600, 200mM zinc acetate, 100mM imidazol pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 18161 / Num. obs: 17336 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.35 % / Biso Wilson estimate: 30.407 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.065 / Net I/σ(I): 14.4
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 4.2 / Num. measured obs: 2149 / Num. unique all: 1333 / Num. unique obs: 978 / Rsym value: 0.261 / % possible all: 73.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WA8

1wa8


Resolution: 2.15→19.858 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.847 / Cross valid method: THROUGHOUT / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 844 5.03 %Random
Rwork0.199 ---
all-16786 --
obs-16786 93.25 %-
Solvent computationBsol: 61.173 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 166.54 Å2 / Biso mean: 30.573 Å2 / Biso min: 11.89 Å2
Baniso -1Baniso -2Baniso -3
1--11.253 Å20 Å20.645 Å2
2--4.299 Å2-0 Å2
3---6.953 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 12 308 2640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.342
X-RAY DIFFRACTIONf_bond_d0.023
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.15-2.1730.209360X-RAY DIFFRACTION3263
2.173-2.1970.244348X-RAY DIFFRACTION3265
2.197-2.2220.218362X-RAY DIFFRACTION3270
2.222-2.2480.197421X-RAY DIFFRACTION3273
2.248-2.2750.189412X-RAY DIFFRACTION3279
2.275-2.3040.205431X-RAY DIFFRACTION3278
2.304-2.3340.199470X-RAY DIFFRACTION3284
2.334-2.3660.199514X-RAY DIFFRACTION3288
2.366-2.40.21526X-RAY DIFFRACTION3293
2.4-2.4360.201496X-RAY DIFFRACTION3291
2.436-2.4740.203477X-RAY DIFFRACTION3292
2.474-2.5140.208508X-RAY DIFFRACTION3292
2.514-2.5570.208526X-RAY DIFFRACTION3292
2.557-2.6040.212513X-RAY DIFFRACTION3293
2.604-2.6540.212531X-RAY DIFFRACTION3292
2.654-2.7080.199509X-RAY DIFFRACTION3292
2.708-2.7660.202501X-RAY DIFFRACTION3294
2.766-2.8310.188526X-RAY DIFFRACTION3292
2.831-2.9010.196523X-RAY DIFFRACTION3293
2.901-2.9790.198541X-RAY DIFFRACTION3293
2.979-3.0670.18498X-RAY DIFFRACTION3293
3.067-3.1650.201512X-RAY DIFFRACTION3293
3.165-3.2780.184532X-RAY DIFFRACTION3294
3.278-3.4090.171554X-RAY DIFFRACTION3294
3.409-3.5630.165509X-RAY DIFFRACTION3294
3.563-3.750.157541X-RAY DIFFRACTION3295
3.75-3.9830.17566X-RAY DIFFRACTION3294
3.983-4.2870.173504X-RAY DIFFRACTION3294
4.287-4.7130.174559X-RAY DIFFRACTION3294
4.713-5.3830.207529X-RAY DIFFRACTION3292
5.383-6.7380.259558X-RAY DIFFRACTION3293
6.738-19.7810.238585X-RAY DIFFRACTION3293
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1602-0.1084-0.01830.52070.1138-0.17740.0564-0.16390.19890.0215-0.0621-0.0687-0.07670.01640.24990.00940.01010.2813-0.00370.298476.125124.424313.9359
20.1090.09530.1280.65160.4026-0.04870.00660.0234-0.19-0.0622-0.00880.02240.04250.02230.224-0.00730.01520.24360.02230.237575.168415.67711.7764
30.19270.01030.16470.3220.02690.4018-0.00060.04190.1211-0.0361-0.00390.0125-0.02580.00480.23350.007-0.00830.2191-0.0110.190633.15769.716830.535
40.12970.0746-0.01650.17660.35240.09990.11750.0465-0.20360.0492-0.0108-0.07420.03180.01320.21190.0113-0.01090.20310.01230.216842.56022.908730.269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 11:84A11 - 84
2X-RAY DIFFRACTION2chain B and resid 10:81B10 - 81
3X-RAY DIFFRACTION3chain C and resid 1:90C1 - 90
4X-RAY DIFFRACTION4chain D and resid 7:84D7 - 84

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