1TUF	Lyase	date	Jun 24, 2004
title	Crystal Structure Of Diaminopimelate Decarboxylase From M. J
authors	K.Rajashankar, S.R.Ray, J.B.Bonanno, M.G.Pinho, G.He, H.De Lencas A.Tomasz, S.K.Burley, New York Sgx Research Center For Struct Genomics (Nysgxrc)
compound		source
Molecule: Diaminopimelate Decarboxylase Chain: A, B Synonym: Dap Decarboxylase Ec: 4.1.1.20 Engineered: Yes		Organism_scientific: Methanocaldococcus Jannaschii Organism_taxid: 2190 Gene: Lysa, Mj1097 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21de3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet T7
symmetry	Space Group: P 61 2 2	R_factor 0.204 R_Free 0.253
crystal cell	length a length b length c angle alpha angle beta angle gamma 80.806 80.806 508.503 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.40 Å
ligand	AZ1, LLP	enzyme	Lyase E.C.4.1.1.20 BRENDA
related structures	by homologous chain: 1TWI
Gene Ontology	Chain Function Process Component A, B
Primary reference	Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor., Ray SS, Bonanno JB, Rajashankar KR, Pinho MG, He G, De Lencastre H, Tomasz A, Burley SK, Structure (Camb) 2002 Nov;10(11):1499-508. PMID:12429091

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (146 Kb) [Save to disk] Biological Unit Coordinates (1tuf.pdb1.gz) 141 Kb Biological Unit Coordinates (1tuf.pdb2.gz) 278 Kb LPC: Ligand-Protein Contacts for 1TUF CSU: Contacts of Structural Units for 1TUF Likely Quarternary Molecular Structure file(s) for 1TUF Structure Factors (521 Kb) Retrieve 1TUF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1TUF from S2C, [Save to disk] Re-refined 1tuf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1TUF 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 1TUF

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 1TUF, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1tufa1, region A:15-49,A:314-448 [Jmol] [rasmolscript] [script source]     - Domain d1tufa2, region A:50-313 [Jmol] [rasmolscript] [script source]     - Domain d1tufb1, region B:15-49,B:314-448 [Jmol] [rasmolscript] [script source]     - Domain d1tufb2, region B:50-313 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1tuf_A] [1tuf_B] [1tuf] SWISS-PROT database: [Q58497] Domain organization of [DCDA_METJA] by SWISSPFAM

Other resources with information on 1TUF

Community annotation for 1TUF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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Images from IMB Jena Image Library of Biological Macromolecules.

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