4HCH | pdb_00004hch

CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS complexed with magnesium and L-tartrate

PDB DOI: https://doi.org/10.2210/pdb4HCH/pdb
Entry: 4HCH supersedes: 3SHH

Classification: ISOMERASE
Organism(s): Agrobacterium fabrum str. C58
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-09-29 Released: 2012-10-24
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sakai, A., Gerlt, J.A., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.171 (Depositor), 0.173 (DCC)
R-Value Work:
0.141 (Depositor), 0.144 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF D-GLUCARATE DEHYDRATASE FROM AGROBACTERIUM TUMEFACIENS complexed with magnesium and L-tartrate

Fedorov, A.A., Fedorov, E.V., Sakai, A., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 91.75 kDa
Atom Count: 7,166
Modeled Residue Count: 768
Deposited Residue Count: 804
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isomerase/lactonizing enzyme	A, B	402	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: Atu3453
UniProt
Find proteins for Q7CSI0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CSI0 Go to UniProtKB: Q7CSI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7CSI0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain C [auth A] MOL2 format, chain M [auth B] MOL2 format, chain C [auth A] mmCIF format, chain M [auth B] mmCIF format, chain C [auth A]	C [auth A], M [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain C [auth A] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] N [auth B] O [auth B] D [auth A], E [auth A], F [auth A], N [auth B], O [auth B], P [auth B], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A], L [auth A], U [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain U [auth B] Focus chain V [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], R [auth B], S [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain R [auth B] Focus chain S [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain I [auth A] MOL2 format, chain T [auth B] MOL2 format, chain I [auth A] mmCIF format, chain T [auth B] mmCIF format, chain I [auth A]	I [auth A], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain T [auth B] Interactions & Density Focus chain I [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.171 (Depositor), 0.173 (DCC)
R-Value Work: 0.141 (Depositor), 0.144 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.252	α = 90
b = 118.252	β = 90
c = 133.018	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-10-24

Deposition Author(s):

This entry supersedes: 3SHH

Revision History (Full details and data files)

Version 1.0: 2012-10-24
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description