3MZN | pdb_00003mzn

Crystal structure of probable glucarate dehydratase from chromohalobacter salexigens dsm 3043

PDB DOI: https://doi.org/10.2210/pdb3MZN/pdb

Classification: LYASE
Organism(s): Chromohalobacter israelensis DSM 3043
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-12 Released: 2010-05-26
Deposition Author(s): Patskovsky, Y., Toro, R., Rutter, M., Sauder, J.M., Gerlt, J.A., Almo, S.C., Burley, S.K., New York Structural GenomiX Research Consortium (NYSGXRC), New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.189 (Depositor), 0.189 (DCC)
R-Value Work:
0.154 (Depositor)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of Glucarate Dehydratase from Chromohalobacter Salexigens

Patskovsky, Y., Toro, R., Rutter, M., Sauder, J.M., Gerlt, J.A., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 101.32 kDa
Atom Count: 7,819
Modeled Residue Count: 892
Deposited Residue Count: 900
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucarate dehydratase	A, B	450	Chromohalobacter israelensis DSM 3043	Mutation(s): 0 Gene Names: Csal_2481 EC: 4.2.1.40
UniProt
Find proteins for Q1QUN0 (Chromohalobacter israelensis (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11)) Explore Q1QUN0 Go to UniProtKB: Q1QUN0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q1QUN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	C [auth A], D [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth B]	E [auth A], H [auth A], J [auth B], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth B] Focus chain M [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	F [auth A], G [auth A], K [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.189 (Depositor), 0.189 (DCC)
R-Value Work: 0.154 (Depositor)
R-Value Observed: 0.155 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.444	α = 90
b = 154.367	β = 90
c = 164.386	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

New York Structural GenomiX Research Consortium (NYSGXRC)

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Structure summary
Version 1.3: 2018-11-21
Changes: Data collection, Structure summary
Version 1.4: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.5: 2024-02-21
Changes: Data collection, Database references