3HYN | pdb_00003hyn

Crystal structure of a putative signal transduction protein (eubrec_0645) from eubacterium rectale atcc 33656 at 1.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3HYN/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Agathobacter rectalis ATCC 33656
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-22 Released: 2009-07-21 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.139 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.117 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.118 (Depositor) 

Literature

Crystal structure of Putative signal transduction protein (YP_002936568.1) from Eubacterium rectale at 1.20 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 22.2 kDa 
• Atom Count: 1,993 
• Modeled Residue Count: 186 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative signal transduction protein	A	189	Agathobacter rectalis ATCC 33656	Mutation(s): 0  Gene Names: YP_002936568.1
UniProt
Find proteins for C4ZCS9 (Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)) Explore C4ZCS9  Go to UniProtKB:  C4ZCS9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRD	B [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-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: 1.20 Å
• R-Value Free:  0.139 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.117 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.118 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33HYN

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.797	α = 90
b = 60.962	β = 90
c = 76.701	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: 2009-07-21 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary