3BF4 | pdb_00003bf4

Crystal structure of an ethd-like protein (reut_b5694) from ralstonia eutropha jmp134 at 2.10 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3BF4/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Cupriavidus pinatubonensis JMP134
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-20 Released: 2007-12-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of EthD-like protein (YP_299883.1) from Ralstonia eutropha JMP134 at 2.10 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.46 kDa 
• Atom Count: 1,964 
• Modeled Residue Count: 226 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ethyl tert-butyl ether degradation EthD protein	A, B	127	Cupriavidus pinatubonensis JMP134	Mutation(s): 3  Gene Names: YP_299883.1, Reut_B5694
UniProt
Find proteins for Q46P95 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46P95  Go to UniProtKB:  Q46P95

Small Molecules

Ligands 2 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
IPA	H [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-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: 2.10 Å
• R-Value Free:  0.212 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33BF4

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.54	α = 90
b = 74.54	β = 90
c = 98.87	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-12-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-01-25
  Changes: Database references
• Version 1.6: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary