3S25 | pdb_00003s25

Crystal structure of a 7-bladed beta-propeller-like protein (EUBREC_1955) from Eubacterium rectale ATCC 33656 at 1.88 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3S25/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Agathobacter rectalis ATCC 33656
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-16 Released: 2011-06-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.183 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Literature

Crystal structure of a Hypothetical 7-bladed beta-propeller-like protein (EUBREC_1955, ERE_32420) from Eubacterium rectale at 1.88 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 35.42 kDa 
• Atom Count: 2,696 
• Modeled Residue Count: 295 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical 7-bladed beta-propeller-like protein	A	302	Agathobacter rectalis ATCC 33656	Mutation(s): 0  Gene Names: ERE_32420, EUBREC_1955
UniProt
Find proteins for C4ZBG5 (Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)) Explore C4ZBG5  Go to UniProtKB:  C4ZBG5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.88 Å
• R-Value Free:  0.183 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33S25

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.649	α = 90
b = 118.649	β = 90
c = 53.892	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Structure summary
• Version 1.3: 2011-11-16
  Changes: Structure summary
• Version 1.4: 2014-12-24
  Changes: Structure summary
• Version 1.5: 2017-11-08
  Changes: Refinement description
• Version 1.6: 2018-01-24
  Changes: Database references
• Version 1.7: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary