4MMW | pdb_00004mmw

Crystal structure of D-glucarate dehydratase from Agrobacterium tumefaciens complexed with magnesium, L-Xylarohydroxamate and L-Lyxarohydroxamate

PDB DOI: https://doi.org/10.2210/pdb4MMW/pdb

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

Deposited: 2013-09-09 Released: 2013-09-18
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: 1.65 Å
R-Value Free:
0.194 (Depositor), 0.195 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of D-glucarate dehydratase from Agrobacterium tumefaciens complexed with magnesium, L-Xylarohydroxamate and L-Lyxarohydroxamate

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

To be published.

Macromolecule Content

Total Structure Weight: 92.41 kDa
Atom Count: 6,920
Modeled Residue Count: 762
Deposited Residue Count: 810
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	405	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LLH Query on LLH Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain G [auth A] MOL2 format, chain R [auth B] MOL2 format, chain G [auth A] mmCIF format, chain R [auth B] mmCIF format, chain G [auth A]	G [auth A], R [auth B]	(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID C₅ H₉ N O₇ DMGBHBFPSRKPBV-ZVHKOUPVSA-N		Interactions Focus chain G [auth A] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain R [auth B]
XYH Query on XYH Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain F [auth A]	F [auth A], Q [auth B]	XYLAROHYDROXAMATE C₅ H₈ N O₇ DMGBHBFPSRKPBV-XZIMBLGRSA-M		Interactions Focus chain F [auth A] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain Q [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] N [auth B] O [auth B] C [auth A], D [auth A], E [auth A], N [auth B], O [auth B], P [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.194 (Depositor), 0.195 (DCC)
R-Value Work: 0.170 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.099	α = 90
b = 118.099	β = 90
c = 133.278	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-09-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-09-18
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description