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)

wwPDB Validation 3D Report Full Report

Validation slider image for 3HYN

This is version 1.4 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4ZCS9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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:

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

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Entry History

Deposition Data

Released Date: 2009-07-21

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.