3D82

Crystal structure of a cupin-2 domain containing protein (sfri_3543) from shewanella frigidimarina ncimb 400 at 2.05 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3D82/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Shewanella frigidimarina NCIMB 400
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-22 Released: 2008-06-10 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.212 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 

Literature

Crystal structure of Domain of Unknown Function with a Cupin Fold (YP_752209.1) from SHEWANELLA FRIGIDIMARINA NCIMB 400 at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.89 kDa 
• Atom Count: 4,532 
• Modelled Residue Count: 508 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin 2, conserved barrel domain protein	A, B, C, D, E	102	Shewanella frigidimarina NCIMB 400	Mutation(s): 0  Gene Names: YP_752209.1, Sfri_3543
UniProt
Find proteins for Q07X94 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q07X94  Go to UniProtKB:  Q07X94

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	N [auth D], Q [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	F [auth A], H [auth B], J [auth C], L [auth D], O [auth E]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
UNL	G [auth A], I [auth B], K [auth C], M [auth D], P [auth E]	Unknown ligand VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.212 
• R-Value Work: 0.186 
• R-Value Observed: 0.187 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M33D82

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.92	α = 90
b = 95.14	β = 90
c = 237.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-10 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-06-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations