3PVZ

UDP-N-acetylglucosamine 4,6-dehydratase from Vibrio fischeri

PDB DOI: https://doi.org/10.2210/pdb3PVZ/pdb
Entry: 3PVZ supersedes: 3NZO

Classification: LYASE
Organism(s): Aliivibrio fischeri ES114
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-12-07 Released: 2011-01-12
Deposition Author(s): Osipiuk, J., Marshall, N., Tesar, C., Pearson, L., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.233
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

UDP-N-acetylglucosamine 4,6-dehydratase from Vibrio fischeri.

Osipiuk, J., Marshall, N., Tesar, C., Pearson, L., Buck, K., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 187.55 kDa
Atom Count: 12,086
Modelled Residue Count: 1,414
Deposited Residue Count: 1,596
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-acetylglucosamine 4,6-dehydratase	A, B, C, D	399	Aliivibrio fischeri ES114	Mutation(s): 0 Gene Names: VF_0140 EC: 4.2.1
UniProt
Find proteins for Q5E8L1 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5E8L1 Go to UniProtKB: Q5E8L1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5E8L1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	E [auth A], K [auth B], L [auth C], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	F [auth A], G [auth A], M [auth C], O [auth D], P [auth D]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.233
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.92	α = 102.71
b = 74.837	β = 95.15
c = 88.789	γ = 100.35

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing