6OXM | pdb_00006oxm

Crystal structure of L,L-diaminopimelate aminotransferase (DapL) from Verrucomicrobium spinosum

PDB DOI: https://doi.org/10.2210/pdb6OXM/pdb

Classification: TRANSFERASE
Organism(s): Verrucomicrobium spinosum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2019-05-13 Released: 2020-07-01
Deposition Author(s): Weatherhead, A., Meng, Y., Dobson, R., Hudson, A.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.189 (Depositor), 0.200 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Characterization of Diaminopimelate Aminotransferase from Verrucomicrobium Spinosum

Weatherhead, A.W., Meng, Y., Dobson, R., Hudson, A.

To be published.

Macromolecule Content

Total Structure Weight: 89.84 kDa
Atom Count: 6,675
Modeled Residue Count: 808
Deposited Residue Count: 822
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate aminotransferase	A, B	411	Verrucomicrobium spinosum	Mutation(s): 0 EC: 2.6.1.83
UniProt
Find proteins for A0A6P3CW87 (Verrucomicrobium spinosum) Explore A0A6P3CW87 Go to UniProtKB: A0A6P3CW87
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6P3CW87
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.189 (Depositor), 0.200 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.05	α = 90
b = 121.372	β = 102.01
c = 76.545	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Weatherhead, A.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1120541
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R15GM120653

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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.