3JZV | pdb_00003jzv

Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2 domain.

PDB DOI: https://doi.org/10.2210/pdb3JZV/pdb

Classification: structural genomics, unknown function
Organism(s): Rhodospirillum rubrum ATCC 11170
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-09-24 Released: 2009-10-13
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.278 (Depositor), 0.272 (DCC)
R-Value Work:
0.225 (Depositor), 0.224 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3JZV

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

Literature

Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2 domain.

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 18.65 kDa
Atom Count: 1,156
Modeled Residue Count: 148
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein Rru_A2000	A	166	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0 Gene Names: Rru_A2000 EC: 2.8.4.6
UniProt
Find proteins for Q2RSU5 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RSU5 Go to UniProtKB: Q2RSU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2RSU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN 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]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-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: 2.30 Å
R-Value Free: 0.278 (Depositor), 0.272 (DCC)
R-Value Work: 0.225 (Depositor), 0.224 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.886	α = 90
b = 90.886	β = 90
c = 161.252	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-10-30
Changes: Data collection, Database references, 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.