3EBR

Crystal structure of an rmlc-like cupin protein (reut_a0381) from ralstonia eutropha jmp134 at 2.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3EBR/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Cupriavidus pinatubonensis JMP134
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-28 Released: 2008-09-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.262 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 

Literature

Crystal structure of RmlC-like cupin with unknown function (YP_294607.1) from RALSTONIA EUTROPHA JMP134 at 2.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 18.69 kDa 
• Atom Count: 1,288 
• Modelled Residue Count: 157 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized RmlC-like cupin	A	159	Cupriavidus pinatubonensis JMP134	Mutation(s): 0  Gene Names: YP_294607.1, Reut_A0381
UniProt
Find proteins for Q476C0 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q476C0  Go to UniProtKB:  Q476C0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A], C [auth A], D [auth A], E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.262 
• R-Value Work: 0.227 
• R-Value Observed: 0.229 
• Space Group: P 4₂ 2 2
• Diffraction Data: https://doi.org/10.18430/M33EBR

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.157	α = 90
b = 91.157	β = 90
c = 48.753	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHARP	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Data collection, 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