3DM8 | pdb_00003dm8

Crystal Structure of Putative Isomerase from Rhodopseudomonas palustris

PDB DOI: https://doi.org/10.2210/pdb3DM8/pdb

Classification: structural genomics, unknown function
Organism(s): Rhodopseudomonas palustris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-06-30 Released: 2008-08-05
Deposition Author(s): Cymborowski, M., Chruszcz, M., Skarina, T., Kagan, O., Savchenko, A., Edwards, A.M., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.216 (Depositor)
R-Value Work:
0.178 (Depositor)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3DM8

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Putative Isomerase from Rhodopseudomonas palustris

Cymborowski, M., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 16.94 kDa
Atom Count: 1,280
Modeled Residue Count: 135
Deposited Residue Count: 143
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein RPA4348	A	143	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA4348
UniProt
Find proteins for Q6N1Q6 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N1Q6 Go to UniProtKB: Q6N1Q6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N1Q6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CE9 Query on CE9 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]	DODECYL NONA ETHYLENE GLYCOL ETHER C₃₀ H₆₂ O₁₀ ONJQDTZCDSESIW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.216 (Depositor)
R-Value Work: 0.178 (Depositor)
R-Value Observed: 0.180 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.593	α = 90
b = 84.071	β = 90
c = 97.211	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data scaling
DM	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Cymborowski, M.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-02-21
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.