2GWG | pdb_00002gwg

Crystal Structure of 4-Oxalomesaconate Hydratase, LigJ, from Rhodopseudomonas palustris, Northeast Structural Genomics Target RpR66.

PDB DOI: https://doi.org/10.2210/pdb2GWG/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Rhodopseudomonas palustris CGA009
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2006-05-04 Released: 2006-05-23
Deposition Author(s): Forouhar, F., Abashidze, M., Jayaraman, S., Cunningham, K., Ciao, M., Ma, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.208 (Depositor), 0.219 (DCC)
R-Value Work:
0.181 (Depositor), 0.194 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of 4-Oxalomesaconate Hydratase, LigJ, from Rhodopseudomonas palustris, Northeast Structural Genomics Target RpR66

Forouhar, F., Abashidze, M., Jayaraman, S., Cunningham, K., Ciao, M., Ma, L., Xiao, R., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

To be published.

Macromolecule Content

Total Structure Weight: 80.24 kDa
Atom Count: 5,836
Modeled Residue Count: 655
Deposited Residue Count: 700
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-oxalomesaconate hydratase	A, B	350	Rhodopseudomonas palustris CGA009	Mutation(s): 10 Gene Names: ligJ, RPA4697, GeneID:2691710
UniProt
Find proteins for Q6N0R4 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N0R4 Go to UniProtKB: Q6N0R4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6N0R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.208 (Depositor), 0.219 (DCC)
R-Value Work: 0.181 (Depositor), 0.194 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.086	α = 90
b = 55.335	β = 90.26
c = 97.166	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-05-23

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2006-05-23
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary