PDB-9hav: F420-dependent glucose-6-phosphate dehydrogenase from Thermomicro...

ID or keywords:

Entry

Database: PDB / ID: 9hav

Title

F420-dependent glucose-6-phosphate dehydrogenase from Thermomicrobium roseus with glucose

Components

Luciferase family protein

Keywords

OXIDOREDUCTASE / glucose / dehydrogenase / F420

Function / homology

F420-dependent glucose-6-phosphate dehydrogenase-related / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / beta-D-glucopyranose / Luciferase family protein

Function and homology information

Biological species

Thermomicrobium roseum DSM 5159 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.22 Å

Authors

Palm, G.J. / Berndt, L. / Lammers, M.

Funding support

1items

Citation

Journal: To Be Published
Title: Discovery of a coenzyme F420-dependent glucose-6-phosphate dehydrogenase from Thermomicrobium roseum
Authors: Last, D. / Hasan, M. / Memman, J.L. / Kroeber, T.D.U. / Palm, G.J. / Lammers, M. / Lackner, G.

History

Deposition	Nov 5, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 19, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hav.cif.gz	1.8 MB	Display	PDBx/mmCIF format
PDB format	pdb9hav.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	9hav.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9hav_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	9hav_full_validation.pdf.gz	2.2 MB	Display
Data in XML	9hav_validation.xml.gz	86.2 KB	Display
Data in CIF	9hav_validation.cif.gz	115.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/9hav ftp://data.pdbj.org/pub/pdb/validation_reports/ha/9hav	HTTPS FTP

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Related structure data

Related structure data	9hawC 9haxC 9hayC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (3) #198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Luciferase family protein

B: Luciferase family protein

C: Luciferase family protein

F: Luciferase family protein

E: Luciferase family protein

D: Luciferase family protein

hetero molecules

255 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, point group 32 (Hermann-Mauguin)

Unit cell

Length a, b, c (Å)	87.767, 154.89, 173.459
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	2 - 335	35 - 368
2	1	1	ALA	ALA	2 - 335	35 - 368
3	2	2	ALA	ALA	1 - 335	34 - 368
4	2	2	ALA	ALA	1 - 335	34 - 368
5	3	3	ALA	ALA	1 - 335	34 - 368
6	3	3	ALA	ALA	1 - 335	34 - 368
7	4	4	ALA	ALA	1 - 335	34 - 368
8	4	4	ALA	ALA	1 - 335	34 - 368
9	5	5	ALA	ALA	1 - 335	34 - 368
10	5	5	ALA	ALA	1 - 335	34 - 368
11	6	6	ALA	ALA	2 - 335	35 - 368
12	6	6	ALA	ALA	2 - 335	35 - 368
13	7	7	ALA	ALA	2 - 335	35 - 368
14	7	7	ALA	ALA	2 - 335	35 - 368
15	8	8	ALA	ALA	2 - 335	35 - 368
16	8	8	ALA	ALA	2 - 335	35 - 368
17	9	9	ALA	ALA	2 - 335	35 - 368
18	9	9	ALA	ALA	2 - 335	35 - 368
19	10	10	GLN	GLN	1 - 336	34 - 369
20	10	10	GLN	GLN	1 - 336	34 - 369
21	11	11	GLN	GLN	1 - 336	34 - 369
22	11	11	GLN	GLN	1 - 336	34 - 369
23	12	12	GLN	GLN	1 - 336	34 - 369
24	12	12	GLN	GLN	1 - 336	34 - 369
25	13	13	GLN	GLN	1 - 336	34 - 369
26	13	13	GLN	GLN	1 - 336	34 - 369
27	14	14	GLN	GLN	1 - 336	34 - 369
28	14	14	GLN	GLN	1 - 336	34 - 369
29	15	15	GLN	GLN	1 - 336	34 - 369
30	15	15	GLN	GLN	1 - 336	34 - 369

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein

Luciferase family protein / F420-dependent glucose-6-phosphate dehydrogenase

Mass: 42305.039 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: F420-dependent glucose-6-phosphate dehydrogenase
Source: (gene. exp.)

Thermomicrobium roseum DSM 5159 (bacteria)
Strain: DSM 5159 / Gene: trd_A0676 / Plasmid: pTK005 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9L4G2

#2: Sugar

ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-NA / SODIUM ION

Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Crystallization: 16% PEG4000, 0.1 M Tris pH 8.5, 0.2 M NaOAc (Jena Bioscience screen 2, B2), Cryocondition: 15% PEG4000, 10% PEG400, 0.1 M Tris pH 8.5, 0.2 M NaOAc

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2020
Radiation	Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.22→50 Å / Num. obs: 117277 / % possible obs: 99.8 % / Redundancy: 6.7 % / B_iso Wilson estimate: 54.2 Å² / R_sym value: 0.107 / Net I/σ(I): 13.4
Reflection shell	Resolution: 2.22→2.35 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 18580 / R_sym value: 1.737 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS	Jan 31, 2020	data reduction
XDS	Jan 31, 2020	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.22→48.33 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.957 / SU B: 15.596 / SU ML: 0.177 / Cross valid method: FREE R-VALUE / ESU R: 0.246 / ESU R Free: 0.184
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2102	5879	5.013 %
R_work	0.1777	111398	-
all	0.179	-	-
obs	-	117277	99.825 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 62.487 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.882 Å²	0 Å²	-0 Å²
2-	-	0.844 Å²	-0 Å²
3-	-	-	-2.727 Å²

Refinement step

Cycle: LAST / Resolution: 2.22→48.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16011	0	76	618	16705

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	16602
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	15446
X-RAY DIFFRACTION	r_angle_refined_deg	1.601	1.831	22563
X-RAY DIFFRACTION	r_angle_other_deg	0.536	1.754	35474
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.5	5	2021
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.173	5	157
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.659	10	2593
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.059	10	812
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	2347
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	20214
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4126
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	3230
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	14110
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	7871
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	8419
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	691
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.121	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.296	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.271	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.297	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	2.562	2.977	8087
X-RAY DIFFRACTION	r_mcbond_other	2.562	2.977	8087
X-RAY DIFFRACTION	r_mcangle_it	3.633	5.346	10107
X-RAY DIFFRACTION	r_mcangle_other	3.633	5.347	10108
X-RAY DIFFRACTION	r_scbond_it	3.339	3.265	8515
X-RAY DIFFRACTION	r_scbond_other	3.339	3.265	8516
X-RAY DIFFRACTION	r_scangle_it	4.988	5.857	12456
X-RAY DIFFRACTION	r_scangle_other	4.987	5.857	12457
X-RAY DIFFRACTION	r_lrange_it	7.239	29.051	18100
X-RAY DIFFRACTION	r_lrange_other	7.228	28.897	17996
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.04	0.05	11516
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.049	0.05	11474
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.048	0.05	11455
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.049	0.05	11472
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.048	0.05	11495
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.046	0.05	11338
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.044	0.05	11321
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.044	0.05	11357
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.043	0.05	11363
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.045	0.05	11499
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.05	0.05	11446
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.048	0.05	11470
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.045	0.05	11343
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.043	0.05	11372
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.043	0.05	11417

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.04013	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.04013	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.0492	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.0492	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.04756	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.04756	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.04869	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.04869	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.04815	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.04815	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.04603	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.04603	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.04388	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.04388	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.04362	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.04362	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.04264	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.04264	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.04471	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.04471	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.04966	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.04966	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.04842	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.04842	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.04535	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.04535	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.04326	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.04326	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.04347	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.04347	0.0501

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.22-2.276	0.354	427	0.381	7997	X-RAY DIFFRACTION	97.9991
2.276-2.338	0.35	384	0.331	7948	X-RAY DIFFRACTION	100
2.338-2.406	0.34	412	0.312	7744	X-RAY DIFFRACTION	99.9877
2.406-2.48	0.316	426	0.283	7458	X-RAY DIFFRACTION	100
2.48-2.561	0.283	361	0.248	7319	X-RAY DIFFRACTION	100
2.561-2.65	0.274	390	0.242	7054	X-RAY DIFFRACTION	100
2.65-2.75	0.264	349	0.216	6835	X-RAY DIFFRACTION	99.9861
2.75-2.862	0.24	354	0.198	6541	X-RAY DIFFRACTION	99.971
2.862-2.989	0.224	364	0.192	6285	X-RAY DIFFRACTION	100
2.989-3.134	0.23	333	0.187	6036	X-RAY DIFFRACTION	99.9843
3.134-3.303	0.212	303	0.188	5741	X-RAY DIFFRACTION	99.9669
3.303-3.502	0.218	279	0.193	5461	X-RAY DIFFRACTION	99.9826
3.502-3.743	0.223	273	0.183	5132	X-RAY DIFFRACTION	100
3.743-4.04	0.172	254	0.149	4820	X-RAY DIFFRACTION	100
4.04-4.423	0.165	228	0.122	4445	X-RAY DIFFRACTION	100
4.423-4.94	0.161	201	0.114	4039	X-RAY DIFFRACTION	100
4.94-5.694	0.167	189	0.132	3566	X-RAY DIFFRACTION	100
5.694-6.95	0.171	144	0.135	3090	X-RAY DIFFRACTION	99.9073
6.95-9.728	0.119	132	0.114	2432	X-RAY DIFFRACTION	100
9.728-48.33	0.232	76	0.198	1455	X-RAY DIFFRACTION	99.4802

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.2387	-0.2164	0.5912	0.9058	-0.2864	1.459	0.0531	-0.1897	-0.1258	0.0008	0.0217	-0.024	0.0719	0.0258	-0.0748	0.0179	0.0047	0.0121	0.0464	0.0163	0.1777	16.7981	-32.3162	-12.3419
2	1.3637	-0.1747	0.3082	0.957	0.2905	1.9904	0.1745	0.4286	0.0255	-0.4426	-0.1	-0.1103	-0.1216	0.5337	-0.0745	0.2559	0.0861	0.0452	0.2549	0.0025	0.1748	20.8545	-26.5817	-45.9358
3	1.4101	-0.0722	0.4176	0.8326	0.2032	2.005	0.2093	0.0398	-0.3364	-0.3343	-0.017	0.3138	0.3199	-0.4761	-0.1923	0.45	0.1028	-0.2287	0.281	0.0372	0.3535	-21.5863	-27.8083	-56.2738
4	1.1084	-0.3253	0.2738	1.0713	0.4185	1.8953	-0.0118	-0.2238	0.3366	-0.015	0.1087	-0.1781	-0.6992	0.1159	-0.0969	0.4725	0.0578	0.0875	0.1571	-0.1084	0.3102	4.3404	8.3829	-2.324
5	1.4381	-0.4969	0.0675	1.0585	0.3039	1.0272	0.0897	-0.2518	0.0097	0.0263	-0.0871	0.4343	-0.272	-0.636	-0.0026	0.3501	0.3185	0.0621	0.5439	-0.0404	0.3902	-29.2932	3.6208	-7.3908
6	0.8865	-0.3352	0.2407	0.8849	0.0482	1.269	0.0005	0.0203	0.3112	-0.28	0.0213	0.2313	-0.5055	-0.4103	-0.0217	0.5768	0.3621	-0.1088	0.3439	0.0563	0.3991	-27.8442	5.4744	-51.026

Refinement TLS group

Selection: ALL

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