PDB-9vw7: NAD(P)-dependent oxidoreductase from Kutzneria albida

ID or keywords:

Entry

Database: PDB / ID: 9vw7

Title

NAD(P)-dependent oxidoreductase from Kutzneria albida

Components

Dehydrogenase

Keywords

OXIDOREDUCTASE / imine reductase

Function / homology

Function and homology information

NADP binding / oxidoreductase activity
Similarity search - Function

Biological species

Kutzneria albida DSM 43870 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.499 Å

Authors

Huang, L. / Fu, H.G. / Yao, Z.C.

Funding support

1items

Citation

Journal: To Be Published
Title: Engineering an Imine Reductase for Enantioselective Synthesis of Atropisomeric Amides
Authors: Huang, L. / Fu, H.G. / Song, D.Q. / Yao, Z.C. / Meng, R.Z. / Zhou, Z.T. / Yu, L.Y. / Wu, Z.Y.

History

Deposition	Jul 16, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jul 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9vw7.cif.gz	130.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9vw7.ent.gz	95.7 KB	Display	PDB format
PDBx/mmJSON format	9vw7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9vw7_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	9vw7_full_validation.pdf.gz	1.3 MB	Display
Data in XML	9vw7_validation.xml.gz	29.6 KB	Display
Data in CIF	9vw7_validation.cif.gz	40.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vw/9vw7 ftp://data.pdbj.org/pub/pdb/validation_reports/vw/9vw7	HTTPS FTP

-
Related structure data

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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#127 - Jul 2010 Crystallins similarity (1) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Dehydrogenase

B: Dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	117.395, 117.395, 99.569
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

-
Protein , 1 types, 2 molecules AB

#1: Protein	Dehydrogenase Mass: 31741.771 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kutzneria albida DSM 43870 (bacteria) / Gene: KALB_1124 / Production host: Escherichia coli (E. coli) / References: UniProt: W5W0Y1

-
Non-polymers , 5 types, 308 molecules

#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₂₁H₃₀N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO₄
#4: Chemical	ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL Mass: 370.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₁₆H₃₄O₉
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H₂O

-
Details

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: 2.7 Å³/Da / Density % sol: 54.48 %
Crystal grow	Temperature: 279.15 K / Method: vapor diffusion, sitting drop Details: 1.0 M Ammonium Sulfate, 0.1 M HEPES:NaOH pH 7.0, and 0.5% (w/v) PEG 8000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 3, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.499→45.84 Å / Num. obs: 24403 / % possible obs: 98.9 % / Redundancy: 1.9 % / CC_1/2: 0.995 / R_merge(I) obs: 0.057 / Net I/σ(I): 13.3
Reflection shell	Resolution: 2.499→2.59 Å / Num. unique obs: 2234 / CC_1/2: 0.813

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
HKL-3000		data reduction
Aimless		data scaling
MrBUMP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.499→41.54 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.917 / SU B: 8.077 / SU ML: 0.176 / Cross valid method: FREE R-VALUE / ESU R: 0.387 / ESU R Free: 0.257
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2275	1270	5.205 %
R_work	0.1603	23131	-
all	0.164	-	-
obs	-	24401	98.854 %

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: 37.351 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.005 Å²	-0 Å²	-0 Å²
2-	-	-0.005 Å²	-0 Å²
3-	-	-	0.009 Å²

Refinement step

Cycle: LAST / Resolution: 2.499→41.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4086	0	132	302	4520

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	4284
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4078
X-RAY DIFFRACTION	r_angle_refined_deg	1.552	1.633	5850
X-RAY DIFFRACTION	r_angle_other_deg	0.508	1.571	9315
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.598	5	571
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.065	5	40
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.793	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.974	10	606
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.312	10	152
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	694
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5177
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	937
X-RAY DIFFRACTION	r_nbd_refined	0.237	0.2	990
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	3766
X-RAY DIFFRACTION	r_nbtor_refined	0.182	0.2	2152
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2384
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	239
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.166	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.172	0.2	71
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.129	0.2	25
X-RAY DIFFRACTION	r_mcbond_it	3.874	3.788	2290
X-RAY DIFFRACTION	r_mcbond_other	3.873	3.788	2289
X-RAY DIFFRACTION	r_mcangle_it	5.504	6.798	2859
X-RAY DIFFRACTION	r_mcangle_other	5.504	6.798	2860
X-RAY DIFFRACTION	r_scbond_it	5.14	4.323	1994
X-RAY DIFFRACTION	r_scbond_other	5.068	4.309	1984
X-RAY DIFFRACTION	r_scangle_it	7.751	7.718	2991
X-RAY DIFFRACTION	r_scangle_other	7.632	7.691	2980
X-RAY DIFFRACTION	r_lrange_it	8.992	37.581	4904
X-RAY DIFFRACTION	r_lrange_other	9.015	36.906	4844

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
2.499-2.564	0.338	95	0.226	1531	0.232	1785	0.934	0.969	91.0924	0.193
2.564-2.634	0.291	92	0.223	1599	0.227	1729	0.937	0.969	97.8022	0.187
2.634-2.71	0.272	77	0.202	1599	0.205	1694	0.957	0.974	98.9374	0.169
2.71-2.793	0.288	98	0.188	1556	0.194	1656	0.95	0.977	99.8792	0.153
2.793-2.884	0.253	79	0.177	1511	0.181	1590	0.954	0.979	100	0.147
2.884-2.985	0.224	79	0.164	1460	0.168	1539	0.962	0.982	100	0.139
2.985-3.097	0.189	94	0.155	1415	0.158	1509	0.978	0.984	100	0.131
3.097-3.222	0.202	81	0.161	1360	0.163	1442	0.971	0.983	99.9306	0.139
3.222-3.365	0.255	73	0.163	1326	0.168	1399	0.959	0.984	100	0.144
3.365-3.528	0.185	72	0.142	1249	0.144	1321	0.978	0.989	100	0.129
3.528-3.717	0.186	57	0.147	1219	0.149	1276	0.976	0.989	100	0.139
3.717-3.941	0.228	55	0.154	1155	0.157	1210	0.971	0.986	100	0.143
3.941-4.21	0.185	59	0.141	1077	0.144	1136	0.978	0.987	100	0.133
4.21-4.543	0.263	44	0.134	1027	0.138	1073	0.959	0.988	99.8136	0.128
4.543-4.971	0.188	46	0.121	937	0.124	983	0.985	0.991	100	0.116
4.971-5.548	0.275	58	0.167	847	0.173	906	0.96	0.985	99.8896	0.155
5.548-6.387	0.276	34	0.198	774	0.201	808	0.946	0.98	100	0.176
6.387-7.777	0.127	31	0.15	667	0.149	699	0.99	0.988	99.8569	0.143
7.777-10.811	0.161	25	0.114	530	0.116	561	0.985	0.991	98.9305	0.118
10.811-41.54	0.353	21	0.248	292	0.254	359	0.931	0.951	87.1866	0.247

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 308 molecules

-
Details

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 308 molecules

-Details

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 308 molecules

-
Details

-
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