4HYR | pdb_00004hyr

Structure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual static disorder

• PDB DOI: https://doi.org/10.2210/pdb4HYR/pdb

• Classification: LYASE
• Organism(s): Acidaminococcus intestini
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-14 Released: 2013-02-13 
• Deposition Author(s): Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Structure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual static disorder

Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 103.04 kDa 
• Atom Count: 8,028 
• Modeled Residue Count: 873 
• Deposited Residue Count: 904 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucarate dehydratase	A, B	452	Acidaminococcus intestini	Mutation(s): 0  Gene Names: ACDG_00756

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], E [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.916	α = 90
b = 88.916	β = 90
c = 236.218	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
ARP/wARP	model building
HKL2Map	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-13 
Deposition Author(s): Hegde, R.P., Toro, R., Burley, S.K., Almo, S.C., Ramagopal, U.A., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-02-13
  Type: Initial release
  
• Version 1.1: 2013-05-08
  Changes: Other
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary