4HN8

Crystal structure of a putative D-glucarate dehydratase from Pseudomonas mendocina ymp

PDB DOI: https://doi.org/10.2210/pdb4HN8/pdb

Classification: LYASE
Organism(s): Pseudomonas mendocina ymp
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-10-19 Released: 2012-11-07
Deposition Author(s): Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.222
R-Value Work: 0.176
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a putative D-glucarate dehydratase from Pseudomonas mendocina ymp

Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A.

To be published.

Macromolecule Content

Total Structure Weight: 423.91 kDa
Atom Count: 27,164
Modelled Residue Count: 3,412
Deposited Residue Count: 3,784
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glucarate dehydratase	A, B, C, D, E A, B, C, D, E, F, G, H	473	Pseudomonas mendocina ymp	Mutation(s): 0 Gene Names: Pmen_1214 EC: 4.2.1.40
UniProt
Find proteins for A4XRL3 (Pseudomonas mendocina (strain ymp)) Explore A4XRL3 Go to UniProtKB: A4XRL3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4XRL3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth G] SDF format, chain Q [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth H]	I [auth A] J [auth A] K [auth B] L [auth C] M [auth D] I [auth A], J [auth A], K [auth B], L [auth C], M [auth D], N [auth E], O [auth F], P [auth G], Q [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth G] Focus chain Q [auth H]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.222
R-Value Work: 0.176
R-Value Observed: 0.178
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.355	α = 90
b = 148.835	β = 90
c = 198.464	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-11-07

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-11-07
Type: Initial release
Version 1.1: 2015-08-26
Changes: Structure summary
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection

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Deposit Data

Help and Resources

4HN8

Crystal structure of a putative D-glucarate dehydratase from Pseudomonas mendocina ymp

Crystal structure of a putative D-glucarate dehydratase from Pseudomonas mendocina ymp

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)