8CDF | pdb_00008cdf

Structure of glutarate hydroxylase (GlaH) from Escherichia coli at a resolution of 1.8 angstrom obtained as a contaminant during routine use of E. coli as an expression host

• PDB DOI: https://doi.org/10.2210/pdb8CDF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-30 Released: 2023-05-31 
• Deposition Author(s): Adeyeye, A.A., Schubert, W.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Structure of glutarate hydroxylase (GlaH) from Escherichia coli at a resolution of 1.8 angstrom obtained as a contaminant during routine use of E. coli as an expression host

Adeyeye, A.A., Schubert, W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.03 kDa 
• Atom Count: 2,646 
• Modeled Residue Count: 299 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutarate 2-hydroxylase	A	311	Escherichia coli	Mutation(s): 0  Gene Names:  csiD, glaH, ACU57_06710, AM464_04980, BGM66_004646, BJI68_04905, C5N07_05545, CTR35_002510, EIZ93_05365, EL79_1036, FOI11_00325, FOI11_022855, FV293_23215, FWK02_21895, G3V95_09995, GIB53_09245, GJO56_18475, GKF89_16305, GNW61_23135, GRW05_29650, GRW24_16590, GRW56_10550, GRW57_12335, HMV95_03335, J0541_002578, JNP96_20920, NCTC9045_01367, NCTC9073_04720, NCTC9117_01751, SAMEA3751407_03408 EC: 1.14.11.64
UniProt
Find proteins for P76621 (Escherichia coli (strain K12)) Explore P76621  Go to UniProtKB:  P76621

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2 (Subject of Investigation/LOI)	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.132	α = 90
b = 121.132	β = 90
c = 136.487	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Adeyeye, A.A., Schubert, W.

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Funding Organization	Location	Grant Number
Other private	South Africa	--

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection