4HCL | pdb_00004hcl

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

• PDB DOI: https://doi.org/10.2210/pdb4HCL/pdb
• Entry: 4HCL supersedes: 3TU2

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


• Deposited: 2012-09-30 Released: 2012-10-24 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sakai, A., Gerlt, J.A., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.95 kDa 
• Atom Count: 6,756 
• Modeled Residue Count: 768 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LLH	E [auth A], I [auth B]	(2R,3S,4R)-2,3,4-TRIHYDROXY-5-(HYDROXYAMINO)-5-OXOPENTANOIC ACID C5 H9 N O7 DMGBHBFPSRKPBV-ZVHKOUPVSA-N
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	C [auth A], D [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.26	α = 90
b = 118.26	β = 90
c = 133.342	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Sakai, A., Gerlt, J.A., Almo, S.C.
• This entry supersedes: 3TU2

Revision History  

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