4NPB

The crystal structure of thiol:disulfide interchange protein DsbC from Yersinia pestis CO92


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The crystal structure of thiol:disulfide interchange protein DsbC from Yersinia pestis CO92

Tan, K.Zhou, M.Kwon, K.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein disulfide isomerase IIA, B220Yersinia pestis CO92Mutation(s): 0 
Gene Names: dsbCy3275Yersinia pestisYPO0891YP_3587
UniProt
Find proteins for A0A5P8YD62 (Yersinia pestis)
Explore A0A5P8YD62 
Go to UniProtKB:  A0A5P8YD62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P8YD62
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranoseC 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
CsucroseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.894α = 90
b = 141.335β = 90
c = 41.153γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary