3C5O | pdb_00003c5o

Crystal structure of the conserved protein of unknown function RPA1785 from Rhodopseudomonas palustris

PDB DOI: https://doi.org/10.2210/pdb3C5O/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Rhodopseudomonas palustris CGA009
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-02-01 Released: 2008-02-19
Deposition Author(s): Kim, Y., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.271 (Depositor), 0.259 (DCC)
R-Value Work:
0.213 (Depositor), 0.206 (DCC)
R-Value Observed:
0.216 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

The Crystal Structure of the Conserved Protein of Unknown Function RPA1785 from Rhodopseudomonas palustris.

Kim, Y., Evdokimova, E., Kudritska, M., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 70.37 kDa
Atom Count: 5,254
Modeled Residue Count: 604
Deposited Residue Count: 628
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0311 protein RPA1785	A, B, C, D	157	Rhodopseudomonas palustris CGA009	Mutation(s): 0 Gene Names: RPA1785
UniProt
Find proteins for P61167 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore P61167 Go to UniProtKB: P61167
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61167
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth D] MOL2 format, chain E [auth D] mmCIF format, chain E [auth D]	E [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.271 (Depositor), 0.259 (DCC)
R-Value Work: 0.213 (Depositor), 0.206 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.117	α = 90
b = 93.248	β = 90
c = 111.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
RESOLVE	phasing
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-19

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-02-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-11-13
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.