OCA Atlas for 1R2C

1R2C

Photosynthesis

date

Sep 26, 2003

title

Photosynthetic Reaction Center Blastochloris Viridis (Atcc)

authors

R.H.Baxter, N.Ponomarenko, R.Pahl, V.Srajer, K.Moffat, J.R.Norris

compound

source

Molecule: Photosynthetic Reaction Center Cytochrome C Subun Precursor;
Chain: C
Synonym: C558c559

Organism_scientific: Blastochloris Viridis
Organism_taxid: 1079

Molecule: Reaction Center Protein L Chain
Chain: L
Synonym: Photosynthetic Reaction Center L Subunit

Organism_scientific: Blastochloris Viridis
Organism_taxid: 1079

Molecule: Reaction Center Protein M Chain
Chain: M
Synonym: Photosynthetic Reaction Center M Subunit

Organism_scientific: Blastochloris Viridis
Organism_taxid: 1079

Molecule: Reaction Center Protein H Chain
Chain: H
Synonym: Photosynthetic Reaction Center H Subunit

Organism_scientific: Blastochloris Viridis
Organism_taxid: 1079

symmetry

Space Group: P 43 21 2

R_factor

0.202

R_Free

0.228

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
223.500	223.500	112.500	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

2.86 Å

ligand

BCB, BPB, FE2, FME, HEM, LDA, MQ7, NS5, SO4, UQ2

enzyme

related structures

by homologous chain: 7PRC

Gene
Ontology

Chain	Function	Process	Component
C	electron transfer activity
H	electron transporter, transf...
L
M

Primary reference

Time-resolved crystallographic studies of light-induced structural changes in the photosynthetic reaction center., Baxter RH, Ponomarenko N, Srajer V, Pahl R, Moffat K, Norris JR, Proc Natl Acad Sci U S A 2004 Apr 20;101(16):5982-7. Epub 2004 Apr 8. PMID:15073325

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (215 Kb) [Save to disk]

Biological Unit Coordinates (1r2c.pdb1.gz) 202 Kb

Biological Unit Coordinates (1r2c.pdb2.gz) 399 Kb

LPC: Ligand-Protein Contacts for 1R2C

CSU: Contacts of Structural Units for 1R2C

Likely Quarternary Molecular Structure file(s) for 1R2C

Structure Factors (554 Kb)

Retrieve 1R2C in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1R2C from S2C, [Save to disk]

Re-refined 1r2c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1R2C in 3D

Proteopedia, because life has more than 2D.

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.

On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1R2C

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1R2C, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1r2cc_, region C [Jmol] [rasmolscript] [script source]
- Domain d1r2ch2, region H:1-36 [Jmol] [rasmolscript] [script source]
- Domain d1r2ch1, region H:37-258 [Jmol] [rasmolscript] [script source]
- Domain d1r2cl_, region L [Jmol] [rasmolscript] [script source]
- Domain d1r2cm_, region M [Jmol] [rasmolscript] [script source]

Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH

Summaries and structural analyses of PDB data files from PDBSum

Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1r2c_C] [1r2c_L] [1r2c_H] [1r2c_M] [1r2c]

SWISS-PROT database: [P07173] [P06008] [P06009] [P06010]

Domain organization of [CYCR_RHOVI] [RCEH_RHOVI] [RCEL_RHOVI] [RCEM_RHOVI] by SWISSPFAM

Other resources with information on 1R2C

Community annotation for 1R2C at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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