9BWU | pdb_00009bwu

Glutarate L-2-hydroxylase (CsiD/GlaH) from Escherichia coli at 2.20 Angstroms Resolution

PDB DOI: https://doi.org/10.2210/pdb9BWU/pdb

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

Deposited: 2024-05-21 Released: 2025-05-28
Deposition Author(s): Han, Z.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.226 (Depositor), 0.226 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Design of Ferroelectric Protein Crystals via DNA-directed Symmetry Breaking

Han, Z.

To be published.

Macromolecule Content

Total Structure Weight: 37.37 kDa
Atom Count: 2,614
Modeled Residue Count: 290
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutarate 2-hydroxylase	A	324	Escherichia coli	Mutation(s): 0 Gene Names: glaH, EcolC_1047 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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: 2.20 Å
R-Value Free: 0.226 (Depositor), 0.226 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.83	α = 90
b = 123.83	β = 90
c = 139.03	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DMR-2104353

Revision History (Full details and data files)

Version 1.0: 2025-05-28
Type: Initial release

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.