3UDO

Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni

PDB DOI: https://doi.org/10.2210/pdb3UDO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-10-28 Released: 2011-11-09
Deposition Author(s): Tkaczuk, K.L., Chruszcz, M., Blus, B.J., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.217
R-Value Work: 0.176
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni

Tkaczuk, K.L., Chruszcz, M., Blus, B.J., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 40.53 kDa
Atom Count: 2,853
Modelled Residue Count: 355
Deposited Residue Count: 361
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-isopropylmalate dehydrogenase	A	361	Campylobacter jejuni	Mutation(s): 1 Gene Names: leuB, Cj1718c EC: 1.1.1.85
UniProt
Find proteins for Q9PLW0 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q9PLW0 Go to UniProtKB: Q9PLW0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9PLW0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.217
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 4₃ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M3GW20

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.794	α = 90
b = 74.794	β = 90
c = 163.787	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
DM	model building
MLPHARE	phasing
RESOLVE	model building
CCP4	model building
ARP/wARP	model building
REFMAC	refinement
Coot	model building
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary

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Help and Resources

3UDO

Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni

Crystal structure of putative isopropylamlate dehydrogenase from Campylobacter jejuni

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)