3RPT

Crystal structure of the anti-HIV b12 scaffold protein

> Summary

Summary for 3RPT

DescriptorEndoglucanase E-2 (E.C.3.2.1.4)
Functional Keywordsscaffold protein anti-hiv, hydrolase
Biological sourceThermobifida fusca
Total number of polymer chains2
Total molecular weight59748.18
Authors
Chen, L.,Kwong, P.D. (deposition date: 2011-04-27, release date: 2011-12-21)
Primary citation
Azoitei, M.L.,Correia, B.E.,Ban, Y.E.,Carrico, C.,Kalyuzhniy, O.,Chen, L.,Schroeter, A.,Huang, P.S.,McLellan, J.S.,Kwong, P.D.,Baker, D.,Strong, R.K.,Schief, W.R.
Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.
Science, 334:373-376, 2011
PubMed: 22021856
DOI: 10.1126/science.1209368
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.303 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.200200.8%11.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

More Biological unit images

Molmil generated image of 3rpt
no rotation
Molmil generated image of 3rpt
rotated about x axis by 90°
Molmil generated image of 3rpt
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 (3rpt.pdb1.gz [115.26 KB])
Coordinate files for Biological unit (3rpt.pdb2.gz [119.84 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
X, AEndoglucanase E-2polymer28229826.12
UniProt (P26222)
Pfam (PF01341)
Thermobifida fuscaCellulase E-2, Cellulase E2, Endo-1,4-beta-glucanase E-2
SULFATE IONnon-polymer96.11
waterwater18.0357

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight59652.1
Non-Polymers*Number of molecules1
Total molecular weight96.1
All*Total molecular weight59748.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.303 Å)

Cell axes45.86746.24062.282
Cell angles78.5781.8061.11
SpacegroupP 1
Resolution limits26.21 - 1.30
the highest resolution shell value1.319 - 1.303
R-factor0.175
R-work0.17350
the highest resolution shell value0.151
R-free0.20200
the highest resolution shell value0.257
RMSD bond length0.011
RMSD bond angle1.251

Data Collection Statistics

Resolution limits50.00 -
the highest resolution shell value -
Completeness79.7
the highest resolution shell value1.7
I/sigma(I)1

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP4.5293

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
A0008810molecular_functioncellulase activity
A0030247molecular_functionpolysaccharide binding
A0030245biological_processcellulose catabolic process
X0008810molecular_functioncellulase activity
X0030247molecular_functionpolysaccharide binding
X0030245biological_processcellulose catabolic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE SO4 A 283
ChainResidue
AHIS41
AASN42
AHIS44
XGLU14
XARG17
XASN18

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

site_idNumber of ResiduesDetails
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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
SWS_FT_FI11Proton donor.
ChainResidueDetails
XNA*

SWS_FT_FI21Nucleophile.
ChainResidueDetails
XASP253

SWS_FT_FI31
ChainResidueDetails
XNA*

SWS_FT_FI41Proton donor.
ChainResidueDetails
ANA*

SWS_FT_FI51Nucleophile.
ChainResidueDetails
AASP253

SWS_FT_FI61
ChainResidueDetails
ANA*

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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

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