3USF | pdb_00003usf

Crystal structure of DAVA-4

PDB DOI: https://doi.org/10.2210/pdb3USF/pdb

Classification: ISOMERASE
Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-11-23 Released: 2012-12-05
Deposition Author(s): Stetefeld, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of DAVA-4

Stetefeld, J.

To be published.

Macromolecule Content

Total Structure Weight: 91.77 kDa
Atom Count: 6,600
Modeled Residue Count: 829
Deposited Residue Count: 854
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate-1-semialdehyde 2,1-aminomutase	A, B	427	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0 EC: 5.4.3.8
UniProt
Find proteins for Q31QJ2 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31QJ2 Go to UniProtKB: Q31QJ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q31QJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLR Query on PLR Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE C₈ H₁₂ N O₅ P RBCOYOYDYNXAFA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
HOZ Query on HOZ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(4S)-4,5-DIAMINOPENTANOIC ACID C₅ H₁₂ N₂ O₂ PQGAAJQIFBEYSA-BYPYZUCNSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.46 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.178 (Depositor), 0.178 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.582	α = 90
b = 108.781	β = 90
c = 124.712	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-05
Type: Initial release
Version 1.1: 2024-02-28
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.