5C6M	Lyase	date	Jun 23, 2015
title	Crystal Structure Of Deoxyribose-Phosphate Aldolase From She Halifaxensis
authors	O.H.Weiergraeber, M.Dick, J.Bramski, J.Pietruszka
compound		source
Molecule: Deoxyribose-Phosphate Aldolase Chain: A, B, C, D Synonym: Dera,2-Deoxy-D-Ribose 5-Phosphate Aldolase, Phosphodeoxyriboaldolase,Deoxyriboaldolase; Ec: 4.1.2.4 Engineered: Yes		Organism_scientific: Shewanella Halifaxensis Organism_taxid: 271098 Gene: Deoc, Shal_3136 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet21a
symmetry	Space Group: C 1 2 1	R_factor 0.168 R_Free 0.198
crystal cell	length a length b length c angle alpha angle beta angle gamma 154.030 52.510 143.210 90.00 122.34 90.00
method	X-Ray Diffraction	resolution	1.76 Å
ligand	CL, NA	enzyme	Lyase E.C.4.1.2.4 BRENDA
Gene	SHAL
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Trading off stability against activity in extremophilic aldolases., Dick M, Weiergraber OH, Classen T, Bisterfeld C, Bramski J, Gohlke H, Pietruszka J, Sci Rep. 2016 Jan 19;6:17908. doi: 10.1038/srep17908. PMID:26783049

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (321 Kb) [Save to disk] Biological Unit Coordinates (5c6m.pdb1.gz) 164 Kb Biological Unit Coordinates (5c6m.pdb2.gz) 154 Kb LPC: Ligand-Protein Contacts for 5C6M CSU: Contacts of Structural Units for 5C6M Structure Factors (823 Kb) Retrieve 5C6M in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5C6M from S2C, [Save to disk] Re-refined 5c6m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5C6M 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 5C6M

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5c6m_B] [5c6m_A] [5c6m_C] [5c6m_D] [5c6m] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5C6M: [DeoC ] by SMART

Other resources with information on 5C6M

Community annotation for 5C6M at PDBWiki (http://pdbwiki.org)

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

---