3DCA

Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target

PDB DOI: https://doi.org/10.2210/pdb3DCA/pdb

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

Deposited: 2008-06-03 Released: 2008-08-05
Deposition Author(s): Sledz, P., Wang, S., Chruszcz, M., Yim, V., Kudritska, M., Evdokimova, E., Turk, D., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.290
R-Value Work: 0.273
R-Value Observed: 0.274

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target

Sledz, P., Wang, S., Chruszcz, M., Yim, V., Kudritska, M., Evdokimova, E., Turk, D., Savchenko, A., Edwards, A., Minor, W.

To be published.

Macromolecule Content

Total Structure Weight: 65.66 kDa
Atom Count: 3,894
Modelled Residue Count: 520
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RPA0582	A, B, C, D	142	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA0582
UniProt
Find proteins for Q6NC90 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NC90 Go to UniProtKB: Q6NC90
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NC90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D]	E [auth A] F [auth A] G [auth B] H [auth C] I [auth D] E [auth A], F [auth A], G [auth B], H [auth C], I [auth D], J [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [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: 3.35 Å
R-Value Free: 0.290
R-Value Work: 0.273
R-Value Observed: 0.274
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.495	α = 90
b = 193.495	β = 90
c = 118.848	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

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: Version format compliance
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

3DCA

Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target

Crystal structure of the RPA0582- protein of unknown function from Rhodopseudomonas palustris- a structural genomics target

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)