5KT0 | pdb_00005kt0

Dihydrodipicolinate reductase from the industrial and evolutionarily important cyanobacteria Anabaena variabilis.

PDB DOI: https://doi.org/10.2210/pdb5KT0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Trichormus variabilis ATCC 29413
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-07-10 Released: 2016-09-07
Deposition Author(s): Christensen, J.B., Soares da Costa, T.P., Faou, P., Pearce, F.G., Panjikar, S., Perugini, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free:
0.243 (Depositor), 0.248 (DCC)
R-Value Work:
0.183 (Depositor), 0.186 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5KT0

This is version 1.2 of the entry. See complete history.

Literature

Dihydrodipicolinate Reductase from the industrial and evolutionarily important cyanobacteria Anabaena variabilis.

Christensen, J.B., Soares da Costa, T.P., Faou, P., Pearce, F.G., Panjikar, S., Perugini, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 33.13 kDa
Atom Count: 2,042
Modeled Residue Count: 274
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-tetrahydrodipicolinate reductase	A	310	Trichormus variabilis ATCC 29413	Mutation(s): 0 Gene Names: dapB, Ava_0474 EC: 1.17.1.8
UniProt
Find proteins for Q3MFY8 (Trichormus variabilis (strain ATCC 29413 / PCC 7937)) Explore Q3MFY8 Go to UniProtKB: Q3MFY8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3MFY8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.243 (Depositor), 0.248 (DCC)
R-Value Work: 0.183 (Depositor), 0.186 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.728	α = 90
b = 89.361	β = 90
c = 95.917	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Christensen, J.B.

Soares da Costa, T.P.

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2017-09-06
Changes: Data collection, Derived calculations
Version 1.2: 2024-03-06
Changes: Data collection, Database references

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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.