PDB-9w7a: Crystal structure of L-galactose dehydrogenase from Luteolibacter...

ID or keywords:

Entry

Database: PDB / ID: 9w7a

Title

Crystal structure of L-galactose dehydrogenase from Luteolibacter sp. strain LG18 in complex with L-glucose and NADP+

Components

L-galactose dehydrogenase

Keywords

OXIDOREDUCTASE / Dehydrogenase

Function / homology

NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / beta-L-glucopyranose

Function and homology information

Biological species

Luteolibacter sp. LG18 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.56 Å

Authors

Koubara, K. / Takenoya, M. / Suzuki, M. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, S.

Funding support

Japan, 1items

Citation

Journal: Biosci.Biotechnol.Biochem. / Year: 2026
Title: Characterization of bacterial l-galactose dehydrogenase with l-glucose dehydrogenase activity from Luteolibacter sp. strain LG18.
Authors: Koubara, K. / Kim, M. / Takenoya, M. / Nakanishi, A. / Suzuki, M. / Azuma, S. / Ito, S. / Sasaki, Y. / Nakamura, A. / Yajima, S.

History

Deposition	Aug 6, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 1, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9w7a.cif.gz	163.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9w7a.ent.gz	121.1 KB	Display	PDB format
PDBx/mmJSON format	9w7a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w7/9w7a ftp://data.pdbj.org/pub/pdb/validation_reports/w7/9w7a	HTTPS FTP

-
Related structure data

Related structure data	9w6yC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: L-galactose dehydrogenase

B: L-galactose dehydrogenase

hetero molecules

77.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: L-galactose dehydrogenase

hetero molecules

defined by author&software
Evidence: homology
38.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: L-galactose dehydrogenase

hetero molecules

defined by author&software
38.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.329, 89.954, 96.200
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

L-galactose dehydrogenase

Mass: 37953.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Luteolibacter sp. LG18 (bacteria) / Production host:

Escherichia coli BL21(DE3) (bacteria)

#2: Sugar

ChemComp-Z8T / beta-L-glucopyranose / beta-L-glucose / L-glucose / glucose

Type: L-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆ / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE

Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 801 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30%(w/v) PEG 8000 200 mM Ammonium sulfate

-
Data collection

Diffraction	Mean temperature: 95 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 19, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.56→48.1 Å / Num. obs: 98431 / % possible obs: 100 % / Redundancy: 6.1 % / CC_1/2: 0.999 / Net I/σ(I): 21.1
Reflection shell	Resolution: 1.56→1.59 Å / Num. unique obs: 4808 / CC_1/2: 0.77

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0431	refinement
XDS		data reduction
pointless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.56→45.017 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.964 / SU B: 1.46 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1838	4860	4.941 %	RANDOM
R_work	0.1596	93493	-	-
all	0.161	-	-	-
obs	-	98353	99.943 %	-

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: 17.931 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.659 Å²	-0 Å²	0 Å²
2-	-	0.438 Å²	0 Å²
3-	-	-	0.221 Å²

Refinement step

Cycle: LAST / Resolution: 1.56→45.017 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4971	0	120	801	5892

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	5210
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4900
X-RAY DIFFRACTION	r_angle_refined_deg	1.496	1.823	7103
X-RAY DIFFRACTION	r_angle_other_deg	0.557	1.738	11302
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.681	5	652
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.18	5	40
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.673	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.427	10	840
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.153	10	221
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	831
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	6074
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1132
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	1153
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.202	0.2	4518
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	2585
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	2597
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	540
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.29	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.273	0.2	42
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.194	0.2	27
X-RAY DIFFRACTION	r_mcbond_it	1.195	1.843	2608
X-RAY DIFFRACTION	r_mcbond_other	1.194	1.843	2608
X-RAY DIFFRACTION	r_mcangle_it	1.686	3.315	3260
X-RAY DIFFRACTION	r_mcangle_other	1.685	3.315	3261
X-RAY DIFFRACTION	r_scbond_it	2.255	2.071	2602
X-RAY DIFFRACTION	r_scbond_other	2.255	2.071	2600
X-RAY DIFFRACTION	r_scangle_it	3.374	3.712	3843
X-RAY DIFFRACTION	r_scangle_other	3.373	3.712	3844
X-RAY DIFFRACTION	r_lrange_it	4.686	21.008	6142
X-RAY DIFFRACTION	r_lrange_other	4.44	19.118	5922

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.56-1.6	0.255	360	0.231	6819	0.232	7208	0.958	0.963	99.5977	0.208
1.6-1.644	0.23	343	0.211	6644	0.212	6994	0.963	0.97	99.8999	0.183
1.644-1.692	0.218	348	0.193	6488	0.195	6837	0.969	0.976	99.9854	0.164
1.692-1.744	0.217	339	0.184	6253	0.186	6592	0.971	0.978	100	0.154
1.744-1.801	0.206	296	0.178	6165	0.179	6461	0.972	0.98	100	0.149
1.801-1.864	0.218	326	0.178	5853	0.18	6179	0.971	0.981	100	0.148
1.864-1.934	0.191	304	0.165	5749	0.166	6053	0.978	0.983	100	0.14
1.934-2.013	0.213	280	0.169	5488	0.171	5768	0.972	0.983	100	0.146
2.013-2.102	0.172	254	0.16	5353	0.16	5608	0.983	0.985	99.9822	0.141
2.102-2.205	0.166	253	0.149	5048	0.149	5301	0.984	0.987	100	0.133
2.205-2.324	0.187	259	0.153	4812	0.155	5073	0.978	0.985	99.9606	0.138
2.324-2.464	0.18	248	0.148	4566	0.15	4814	0.98	0.986	100	0.136
2.464-2.634	0.175	201	0.149	4341	0.15	4543	0.982	0.986	99.978	0.14
2.634-2.844	0.186	223	0.158	4029	0.16	4256	0.979	0.984	99.906	0.151
2.844-3.114	0.176	187	0.155	3705	0.156	3893	0.981	0.985	99.9743	0.154
3.114-3.48	0.166	175	0.159	3388	0.159	3566	0.982	0.986	99.9159	0.161
3.48-4.014	0.143	126	0.14	3028	0.14	3155	0.988	0.989	99.9683	0.149
4.014-4.907	0.154	134	0.131	2562	0.132	2697	0.987	0.991	99.9629	0.144
4.907-6.898	0.209	126	0.174	2006	0.176	2132	0.982	0.986	100	0.186
6.898-45.017	0.189	78	0.175	1196	0.176	1274	0.983	0.981	100	0.2

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi