3FAV

Structure of the CFP10-ESAT6 complex from Mycobacterium tuberculosis

> Summary

Summary for 3FAV

Related1WA8 2VRZ 2VS0
DescriptorESAT-6-like protein esxB, 6 kDa early secretory antigenic target
Functional Keywordscomplex, operon structure, four-helical-bundle, coiled-coil, wxg-motif, mycobacterium tuberculosis, secreted, secretion system, adaptor protein, proposed virulent factor, viral protein
Biological sourceMycobacterium tuberculosis
Total number of polymer chains4
Total molecular weight41829.97
Authors
Poulsen, C.,Holton, S.J.,Wilmanns, M.,Song, Y.H. (deposition date: 2008-11-18, release date: 2009-11-24, modification date: 2014-08-13)
Primary citation
Poulsen, C.,Panjikar, S.,Holton, S.J.,Wilmanns, M.,Song, Y.H.
WXG100 protein superfamily consists of three subfamilies and exhibits an alpha-helical C-terminal conserved residue pattern.
Plos One, 9:e89313-e89313, 2014
PubMed: 24586681
DOI: 10.1371/journal.pone.0089313
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.15 Å)
NMR Information
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.229701.8%6.1%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 3fav
no rotation
Molmil generated image of 3fav
rotated about x axis by 90°
Molmil generated image of 3fav
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 3fav
no rotation
Molmil generated image of 3fav
rotated about x axis by 90°
Molmil generated image of 3fav
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (3fav.pdb1.gz [47.22 KB])
Coordinate files for Biological unit (3fav.pdb2.gz [56.36 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, CESAT-6-like protein esxBpolymer10110873.92
UniProt (P0A566)
Pfam (PF06013)
UniProt (by SIFTS) (P9WNK5)
Mycobacterium tuberculosisCFP-10, 10 kDa culture filtrate antigen cfp10, Secreted antigenic protein MTSA-10
B, D6 kDa early secretory antigenic targetpolymer949777.72
UniProt (P0A564)
Pfam (PF06013)
UniProt (by SIFTS) (P9WNK7)
Mycobacterium tuberculosisESAT-6
ZINC IONnon-polymer65.47
IMIDAZOLEnon-polymer69.11
waterwater18.0308

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight41303.2
Non-Polymers*Number of molecules8
Total molecular weight526.7
All*Total molecular weight41830.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.15 Å)

Cell axes160.34023.93083.860
Cell angles90.0094.3690.00
SpacegroupC 1 2 1
Resolution limits19.86 - 2.15
the highest resolution shell value2.173 - 2.150
R-work0.19900
the highest resolution shell value0.209
R-free0.23300
RMSD bond length0.023
RMSD bond angle1.342

Data Collection Statistics

Resolution limits20.00 - 2.15
the highest resolution shell value -
Number of reflections17336
Rmerge_l_obs0.055
the highest resolution shell value0.197
Completeness95.5
Redundancy3.35
the highest resolution shell value2.2
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.5292

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
B0005618cellular_componentcell wall
B0005737cellular_componentcytoplasm
B0005576cellular_componentextracellular region
B0005886cellular_componentplasma membrane
B0046812molecular_functionhost cell surface binding
B0042803molecular_functionprotein homodimerization activity
B0052027biological_processmodulation by symbiont of host signal transduction pathway
B0052083biological_processnegative regulation by symbiont of host cell-mediated immune response
B0009405biological_processpathogenesis
B0044315biological_processprotein secretion by the type VII secretion system
D0005618cellular_componentcell wall
D0005737cellular_componentcytoplasm
D0005576cellular_componentextracellular region
D0005886cellular_componentplasma membrane
D0046812molecular_functionhost cell surface binding
D0042803molecular_functionprotein homodimerization activity
D0052027biological_processmodulation by symbiont of host signal transduction pathway
D0052083biological_processnegative regulation by symbiont of host cell-mediated immune response
D0009405biological_processpathogenesis
D0044315biological_processprotein secretion by the type VII secretion system
A0005618cellular_componentcell wall
A0005576cellular_componentextracellular region
A0005886cellular_componentplasma membrane
A0046812molecular_functionhost cell surface binding
A0009405biological_processpathogenesis
A0044315biological_processprotein secretion by the type VII secretion system
C0005618cellular_componentcell wall
C0005576cellular_componentextracellular region
C0005886cellular_componentplasma membrane
C0046812molecular_functionhost cell surface binding
C0009405biological_processpathogenesis
C0044315biological_processprotein secretion by the type VII secretion system
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15BINDING SITE FOR RESIDUE ZN A 101
ChainResidue
AGLU14
AASN17
AHOH167
BLYS38
BHOH132

AC22BINDING SITE FOR RESIDUE ZN A 102
ChainResidue
AASP24
AHOH303

AC33BINDING SITE FOR RESIDUE ZN B 1
ChainResidue
BHIS26
BASP30
BHOH308

AC44BINDING SITE FOR RESIDUE ZN B 96
ChainResidue
BGLU31
BGLU31
BIMD97
BIMD97

AC57BINDING SITE FOR RESIDUE IMD B 97
ChainResidue
AARG20
AHOH302
BLEU28
BGLU31
BGLU31
BZN96
BZN96

AC64BINDING SITE FOR RESIDUE ZN C 101
ChainResidue
BGLU49
CGLU3
CASP7
CHOH306

AC74BINDING SITE FOR RESIDUE ZN C 102
ChainResidue
CASP30
CHOH197
CHOH288
DASP30

AC83BINDING SITE FOR RESIDUE ZN D 96
ChainResidue
CGLU33
CHOH201
DHIS26

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
IMD_3fav_B_976IMIDAZOLE binding site
ChainResidueligand
AARG20IMD: IMIDAZOLE
AASP24IMD: IMIDAZOLE
BSER24IMD: IMIDAZOLE
BSER27-LEU28IMD: IMIDAZOLE
BGLU31IMD: IMIDAZOLE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb3fav.ent.gz (108.2 KB)
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all (no-compress)pdb3fav.ent (451.43 KB)
header onlypdb3fav.ent.gz (8.52 KB)
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PDBx/mmCIF3fav.cif.gz (131.78 KB)
PDBMLall3fav.xml.gz (201.81 KB)
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no-atom3fav-noatom.xml.gz (25.12 KB)
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ext-atom3fav-extatom.xml.gz (62.29 KB)
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PDBMLplusall3fav-plus.xml.gz (203.54 KB)
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no-atom3fav-plus-noatom.xml.gz (26.85 KB)
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add only3fav-add.xml.gz (1.72 KB)
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RDF3fav.rdf.gz (46.19 KB)
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Structure factorsr3favsf.ent.gz (159.45 KB)
Biological unit (PDB format)3fav.pdb1.gz (47.22 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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3fav.pdb2.gz (56.36 KB) (C,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF3fav​_validation.pdf.gz (293.14 KB)
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PDF-full3fav​_full​_validation.pdf.gz (297.34 KB)
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XML3fav​_validation.xml.gz (18.88 KB)
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PNG3fav​_multipercentile​_validation.png.gz (148.95 KB)
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SVG3fav​_multipercentile​_validation.svg.gz (931 B)
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Sequence (fasta)3fav​_seq.txt
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