39OZ | pdb_000039oz

Cryo-EM structure of glutamate mutase from Carboxydothermus hydrogenoformans in the pre-activation state

PDB DOI: https://doi.org/10.2210/pdb39OZ/pdb
EM Map EMD-79675: EMDB EMDataResource

Classification: ISOMERASE
Organism(s): Carboxydothermus hydrogenoformans Z-2901
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-10-20 Released: 2026-10-28
Deposition Author(s): Zhang, X.Y., Tjia-Fleck, S.K., Tian, S.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 39OZ

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

Literature

Cryo-EM structure of glutamate mutase from Carboxydothermus hydrogenoformans in the pre-activation state

Zhang, X.Y., Tjia-Fleck, S.K., Tian, S.L.

To be published.

Macromolecule Content

Total Structure Weight: 138.87 kDa
Atom Count: 9,771
Modeled Residue Count: 1,238
Deposited Residue Count: 1,238
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate mutase epsilon subunit	A, B	482	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: mutE, glmE, CHY_0309 EC: 5.4.99.1
UniProt
Find proteins for Q3AFA5 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3AFA5 Go to UniProtKB: Q3AFA5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3AFA5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate mutase sigma subunit	C, D	137	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 0 Gene Names: glmS, mamA, CHY_0307 EC: 5.4.99.1
UniProt
Find proteins for Q3AFA7 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q3AFA7 Go to UniProtKB: Q3AFA7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3AFA7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]
5AD (Subject of Investigation/LOI) Query on 5AD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	5'-DEOXYADENOSINE C₁₀ H₁₃ N₅ O₃ XGYIMTFOTBMPFP-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-28

Deposition Author(s):

Tjia-Fleck, S.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM155016

Revision History (Full details and data files)

Version 1.0: 2026-10-28
Type: Initial release