2VDH	Lyase	date	Oct 09, 2007
title	Crystal Structure Of Chlamydomonas Reinhardtii Rubisco With Subunit C172s Mutation
authors	M.J.Garcia-Murria, S.Karkehabadi, J.Marin-Navarro, S.Satagopan I.Andersson, R.J.Spreitzer, J.Moreno
compound		source
Molecule: Ribulose Bisphosphate Carboxylase Large Chain Chain: A, B, C, D, E, F, G, H Synonym: Ribulose-1,5-Bisphosphate Carboxylase Large Chain, Large Subunit; Ec: 4.1.1.39 Engineered: Yes Mutation: Yes		Organism_scientific: Chlamydomonas Reinhardtii Organism_taxid: 3055 Strain: 18-7g Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_plasmid: Pls-C172s
Molecule: Ribulose Bisphosphate Carboxylase Small Chain 1 Chain: I, J, K, L, M, N, O, P Synonym: Rubisco Small Subunit 1,Ribulose-1,5-Bisphosphate Carboxylase Small Chain; Ec: 4.1.1.39 Engineered: Yes		Organism_scientific: Chlamydomonas Reinhardtii Organism_taxid: 3055 Strain: 18-7g Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_plasmid: Pls-C172s
symmetry	Space Group: P 1 21 1	R_factor 0.171 R_Free 0.203
crystal cell	length a length b length c angle alpha angle beta angle gamma 120.190 178.349 122.561 90.00 117.87 90.00
method	X-Ray Diffraction	resolution	2.30 Å
ligand	CAP, EDO, HYP, KCX, MG, MME, SMC	enzyme	Lyase E.C.4.1.1.39 BRENDA
Gene Ontology	Chain Function Process Component F, A, E, B, H, C, D, G
Primary reference	Structural and functional consequences of the replacement of proximal residues Cys(172) and Cys(192) in the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase from Chlamydomonas reinhardtii., Garcia-Murria MJ, Karkehabadi S, Marin-Navarro J, Satagopan S, Andersson I, Spreitzer RJ, Moreno J, Biochem J. 2008 Apr 15;411(2):241-7. PMID:18072944

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (799 Kb) [Save to disk] Biological Unit Coordinates (2vdh.pdb1.gz) 785 Kb LPC: Ligand-Protein Contacts for 2VDH CSU: Contacts of Structural Units for 2VDH Likely Quarternary Molecular Structure file(s) for 2VDH Structure Factors (1695 Kb) Retrieve 2VDH in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2VDH from S2C, [Save to disk] Re-refined 2vdh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2VDH 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 2VDH

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 2VDH, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2vdh_F] [2vdh_L] [2vdh] [2vdh_A] [2vdh_K] [2vdh_H] [2vdh_B] [2vdh_C] [2vdh_E] [2vdh_G] [2vdh_O] [2vdh_P] [2vdh_D] [2vdh_I] [2vdh_J] [2vdh_N] [2vdh_M] SWISS-PROT database: [P00877] [P00873] Domain organization of [RBL_CHLRE] [RBS1_CHLRE] by SWISSPFAM Domain found in 2VDH: [RuBisCO_small ] by SMART

Other resources with information on 2VDH

Community annotation for 2VDH at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---