3A8U | pdb_00003a8u

Crystal Structure of omega-Amino Acid:Pyruvate Aminotransferase

PDB DOI: https://doi.org/10.2210/pdb3A8U/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas putida
Mutation(s): No

Deposited: 2009-10-11 Released: 2009-11-10
Deposition Author(s): Watanabe, N., Sakabe, N., Sakabe, K., Sasaki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.158 (Depositor), 0.146 (DCC)
R-Value Work:
0.146 (Depositor), 0.147 (DCC)
R-Value Observed:
0.147 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of omega-Amino Acid:Pyruvate Aminotransferase

Watanabe, N., Sakabe, N., Sakabe, K., Sasaki, K.

To be published.

Macromolecule Content

Total Structure Weight: 48.92 kDa
Atom Count: 3,774
Modeled Residue Count: 441
Deposited Residue Count: 449
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Omega-amino acid--pyruvate aminotransferase	A [auth X]	449	Pseudomonas putida	Mutation(s): 0 EC: 2.6.1.18
UniProt
Find proteins for P28269 (Pseudomonas putida) Explore P28269 Go to UniProtKB: P28269
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28269
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.158 (Depositor), 0.146 (DCC)
R-Value Work: 0.146 (Depositor), 0.147 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.46	α = 90
b = 137.79	β = 90
c = 61.57	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.