OCA Atlas for 1MT1

1MT1

Lyase

date

Sep 20, 2002

title

The Crystal Structure Of Pyruvoyl-Dependent Arginine Decarbo From Methanococcus Jannaschii

authors

W.D.Tolbert, D.E.Graham, R.H.White, S.E.Ealick

compound

source

Molecule: Pyruvoyl-Dependent Arginine Decarboxylase Beta Ch
Chain: A, C, E, G, I, K
Ec: 4.1.1.19
Engineered: Yes

Organism_scientific: Methanocaldococcus Jannaschii
Organism_taxid: 2190
Gene: Mj0316
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Codonplus(De3)-Ril (Stratage
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet19b (Novagen)

Molecule: Pyruvoyl-Dependent Arginine Decarboxylase Alpha C
Chain: B, D, F, H, J, L
Ec: 4.1.1.19
Engineered: Yes

symmetry

Space Group: P 1 21 1

R_factor

0.190

R_Free

0.229

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
56.770	92.990	87.230	90.00	94.84	90.00

method

X-Ray Diffraction

resolution

2.20 Å

ligand

AG2, MSE, PYR

enzyme

Lyase E.C.4.1.1.19 BRENDA

related structures

by homologous chain: 1N2M

Gene
Ontology

Chain	Function	Process	Component
A, K, E, C, I, G
F, J, B, H, D, L

Primary reference

Pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii: crystal structures of the self-cleaved and S53A proenzyme forms., Tolbert WD, Graham DE, White RH, Ealick SE, Structure (Camb) 2003 Mar;11(3):285-94. PMID:12623016

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (165 Kb) [Save to disk]

Biological Unit Coordinates (1mt1.pdb1.gz) 82 Kb

Biological Unit Coordinates (1mt1.pdb2.gz) 80 Kb

LPC: Ligand-Protein Contacts for 1MT1

CSU: Contacts of Structural Units for 1MT1

Likely Quarternary Molecular Structure file(s) for 1MT1

Structure Factors (1313 Kb)

Retrieve 1MT1 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1MT1 from S2C, [Save to disk]

Re-refined 1mt1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1MT1 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 1MT1

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 1MT1, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1mt1.1, region A:,B [Jmol] [rasmolscript] [script source]
- Domain d1mt1.2, region C:,D [Jmol] [rasmolscript] [script source]
- Domain d1mt1.3, region E:,F [Jmol] [rasmolscript] [script source]
- Domain d1mt1.4, region G:,H [Jmol] [rasmolscript] [script source]
- Domain d1mt1.5, region I:,J [Jmol] [rasmolscript] [script source]
- Domain d1mt1.6, region K:,L [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: [1mt1_L] [1mt1_B] [1mt1_C] [1mt1_A] [1mt1_K] [1mt1] [1mt1_J] [1mt1_G] [1mt1_D] [1mt1_I] [1mt1_E] [1mt1_F] [1mt1_H]

SWISS-PROT database: [Q57764]

Domain organization of [PDAD_METJA] by SWISSPFAM

Other resources with information on 1MT1

Community annotation for 1MT1 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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