9HAX | pdb_00009hax

F420-dependent glucose-6-phosphate dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb9HAX/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: 2.51 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.231 (Depositor), 0.231 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9HAX

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

To be published.

Macromolecule Content

Total Structure Weight: 511.7 kDa
Atom Count: 32,985
Modeled Residue Count: 4,079
Deposited Residue Count: 4,560
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain ZA [auth I] SDF format, chain YA [auth I] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain VA [auth H] SDF format, chain V [auth C] SDF format, chain UA [auth H] SDF format, chain TA [auth H] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain QA [auth G] SDF format, chain PA [auth G] SDF format, chain OA [auth G] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MB [auth L] SDF format, chain MA [auth F] SDF format, chain M [auth A] SDF format, chain LB [auth L] SDF format, chain LA [auth F] SDF format, chain KB [auth L] SDF format, chain KA [auth F] SDF format, chain IB [auth K] SDF format, chain HB [auth K] SDF format, chain HA [auth E] SDF format, chain GB [auth K] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain DB [auth J] SDF format, chain CB [auth J] SDF format, chain CA [auth D] SDF format, chain BB [auth J] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain ZA [auth I] MOL2 format, chain YA [auth I] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain UA [auth H] MOL2 format, chain TA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MB [auth L] MOL2 format, chain MA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth L] MOL2 format, chain LA [auth F] MOL2 format, chain KB [auth L] MOL2 format, chain KA [auth F] MOL2 format, chain IB [auth K] MOL2 format, chain HB [auth K] MOL2 format, chain HA [auth E] MOL2 format, chain GB [auth K] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain DB [auth J] MOL2 format, chain CB [auth J] MOL2 format, chain CA [auth D] MOL2 format, chain BB [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain ZA [auth I] mmCIF format, chain YA [auth I] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain UA [auth H] mmCIF format, chain TA [auth H] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain PA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MB [auth L] mmCIF format, chain MA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth L] mmCIF format, chain LA [auth F] mmCIF format, chain KB [auth L] mmCIF format, chain KA [auth F] mmCIF format, chain IB [auth K] mmCIF format, chain HB [auth K] mmCIF format, chain HA [auth E] mmCIF format, chain GB [auth K] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain DB [auth J] mmCIF format, chain CB [auth J] mmCIF format, chain CA [auth D] mmCIF format, chain BB [auth J] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] BB [auth J] CA [auth D] CB [auth J] AA [auth D], BA [auth D], BB [auth J], CA [auth D], CB [auth J], DB [auth J], FA [auth E], GA [auth E], GB [auth K], HA [auth E], HB [auth K], IB [auth K], KA [auth F], KB [auth L], LA [auth F], LB [auth L], M [auth A], MA [auth F], MB [auth L], N [auth A], O [auth A], OA [auth G], PA [auth G], QA [auth G], R [auth B], S [auth B], T [auth B], TA [auth H], UA [auth H], V [auth C], VA [auth H], W [auth C], X [auth C], YA [auth I], ZA [auth I]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain BB [auth J] Focus chain CA [auth D] Focus chain CB [auth J] Focus chain DB [auth J] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain GB [auth K] Focus chain HA [auth E] Focus chain HB [auth K] Focus chain IB [auth K] Focus chain KA [auth F] Focus chain KB [auth L] Focus chain LA [auth F] Focus chain LB [auth L] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth L] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain X [auth C] Focus chain YA [auth I] Focus chain ZA [auth I] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain BB [auth J] Focus chain CA [auth D] Focus chain CB [auth J] Focus chain DB [auth J] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain GB [auth K] Focus chain HA [auth E] Focus chain HB [auth K] Focus chain IB [auth K] Focus chain KA [auth F] Focus chain KB [auth L] Focus chain LA [auth F] Focus chain LB [auth L] Focus chain M [auth A] Focus chain MA [auth F] Focus chain MB [auth L] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth H] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Focus chain X [auth C] Focus chain YA [auth I] Focus chain ZA [auth I]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain XA [auth H] SDF format, chain WA [auth H] SDF format, chain U [auth B] SDF format, chain SA [auth G] SDF format, chain RA [auth G] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain NB [auth L] SDF format, chain NA [auth F] SDF format, chain JB [auth K] SDF format, chain JA [auth E] SDF format, chain IA [auth E] SDF format, chain FB [auth J] SDF format, chain EB [auth J] SDF format, chain EA [auth D] SDF format, chain DA [auth D] SDF format, chain AB [auth I] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain XA [auth H] MOL2 format, chain WA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain SA [auth G] MOL2 format, chain RA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain NB [auth L] MOL2 format, chain NA [auth F] MOL2 format, chain JB [auth K] MOL2 format, chain JA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain FB [auth J] MOL2 format, chain EB [auth J] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain AB [auth I] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain XA [auth H] mmCIF format, chain WA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain SA [auth G] mmCIF format, chain RA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain NB [auth L] mmCIF format, chain NA [auth F] mmCIF format, chain JB [auth K] mmCIF format, chain JA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain FB [auth J] mmCIF format, chain EB [auth J] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain AB [auth I]	AB [auth I] DA [auth D] EA [auth D] EB [auth J] FB [auth J] AB [auth I], DA [auth D], EA [auth D], EB [auth J], FB [auth J], IA [auth E], JA [auth E], JB [auth K], NA [auth F], NB [auth L], P [auth A], Q [auth A], RA [auth G], SA [auth G], U [auth B], WA [auth H], XA [auth H], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth I] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain JB [auth K] Focus chain NA [auth F] Focus chain NB [auth L] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain U [auth B] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AB [auth I] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain EB [auth J] Focus chain FB [auth J] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain JB [auth K] Focus chain NA [auth F] Focus chain NB [auth L] Focus chain P [auth A] Focus chain Q [auth A] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain U [auth B] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.257 (Depositor), 0.257 (DCC)
R-Value Work: 0.231 (Depositor), 0.231 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.528	α = 90
b = 239.408	β = 108.588
c = 108.2	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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.