9HAW | pdb_00009haw

F420-dependent glucose-6-phosphate dehydrogenase without ligand

PDB DOI: https://doi.org/10.2210/pdb9HAW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermomicrobium roseum DSM 5159
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-05 Released: 2025-11-19
Deposition Author(s): Palm, G.J., Berndt, L., Lammers, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.193 (Depositor), 0.160 (DCC)
R-Value Work:
0.173 (Depositor), 0.164 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9HAW

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

Literature

Discovery of a coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Thermomicrobium roseum

Last, M., Hasan, M., Hemmann, J.L., Kroeber, T.D.U., Palm, G.J., Lammers, M., Lackner, G.

To be published.

Macromolecule Content

Total Structure Weight: 762.06 kDa
Atom Count: 50,826
Modeled Residue Count: 6,090
Deposited Residue Count: 6,840
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferase family protein	A B C D E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O [auth Q], P [auth R], Q [auth O], R [auth P]	380	Thermomicrobium roseum DSM 5159	Mutation(s): 0 Gene Names: trd_A0676
UniProt
Find proteins for B9L4G2 (Thermomicrobium roseum (strain ATCC 27502 / DSM 5159 / P-2)) Explore B9L4G2 Go to UniProtKB: B9L4G2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9L4G2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth K] SDF format, chain BA [auth L] SDF format, chain CA [auth M] SDF format, chain DA [auth N] SDF format, chain EA [auth Q] SDF format, chain FA [auth R] SDF format, chain GA [auth O] SDF format, chain HA [auth P] SDF format, chain S [auth A] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth E] SDF format, chain W [auth G] SDF format, chain X [auth H] SDF format, chain Y [auth I] SDF format, chain Z [auth J] MOL2 format, chain AA [auth K] MOL2 format, chain BA [auth L] MOL2 format, chain CA [auth M] MOL2 format, chain DA [auth N] MOL2 format, chain EA [auth Q] MOL2 format, chain FA [auth R] MOL2 format, chain GA [auth O] MOL2 format, chain HA [auth P] MOL2 format, chain S [auth A] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth G] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth I] MOL2 format, chain Z [auth J] mmCIF format, chain AA [auth K] mmCIF format, chain BA [auth L] mmCIF format, chain CA [auth M] mmCIF format, chain DA [auth N] mmCIF format, chain EA [auth Q] mmCIF format, chain FA [auth R] mmCIF format, chain GA [auth O] mmCIF format, chain HA [auth P] mmCIF format, chain S [auth A] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth G] mmCIF format, chain X [auth H] mmCIF format, chain Y [auth I] mmCIF format, chain Z [auth J]	AA [auth K] BA [auth L] CA [auth M] DA [auth N] EA [auth Q] AA [auth K], BA [auth L], CA [auth M], DA [auth N], EA [auth Q], FA [auth R], GA [auth O], HA [auth P], S [auth A], T [auth C], U [auth D], V [auth E], W [auth G], X [auth H], Y [auth I], Z [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth Q] Focus chain FA [auth R] Focus chain GA [auth O] Focus chain HA [auth P] Focus chain S [auth A] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain DA [auth N] Focus chain EA [auth Q] Focus chain FA [auth R] Focus chain GA [auth O] Focus chain HA [auth P] Focus chain S [auth A] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth I] Focus chain Z [auth J]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.193 (Depositor), 0.160 (DCC)
R-Value Work: 0.173 (Depositor), 0.164 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 200.482	α = 90
b = 376.876	β = 90
c = 104.772	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-11-19
Type: Initial release

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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.