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

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
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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.

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

Find similar proteins by:

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... 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P76621
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	South Africa	--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.