2PFW | pdb_00002pfw

CRYSTAL STRUCTURE OF A RMLC-LIKE CUPIN (SFRI_3105) FROM SHEWANELLA FRIGIDIMARINA NCIMB 400 AT 1.90 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2PFW/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Shewanella frigidimarina NCIMB 400
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-04-05 Released: 2007-04-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.256 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of Cupin 2 conserved barrel domain protein (YP_751781.1) from Shewanella frigidimarina NCIMB 400 at 1.90 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, light scattering

Macromolecule Content 

• Total Structure Weight: 26.08 kDa 
• Atom Count: 1,880 
• Modeled Residue Count: 223 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin 2, conserved barrel domain protein	A, B	116	Shewanella frigidimarina NCIMB 400	Mutation(s): 3  Gene Names: YP_751781.1, Sfri_3105
UniProt
Find proteins for Q07YH2 (Shewanella frigidimarina (strain NCIMB 400)) Explore Q07YH2  Go to UniProtKB:  Q07YH2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth B], E [auth B], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.256 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32PFW

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.5	α = 90
b = 73.14	β = 90
c = 73.13	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-04-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2017-10-25
  Changes: Author supporting evidence
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-20
  Changes: Data collection, Structure summary