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

ID or keywords:

Entry

Database: PDB / ID: 9vvs

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 /

MOLECULAR REPLACEMENT / Resolution: 2.68 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

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Download

PDBx/mmCIF format	9vvs.cif.gz	126.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9vvs.ent.gz	92.2 KB	Display	PDB format
PDBx/mmJSON format	9vvs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9vvs_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9vvs_full_validation.pdf.gz	1 MB	Display
Data in XML	9vvs_validation.xml.gz	27.4 KB	Display
Data in CIF	9vvs_validation.cif.gz	37.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vv/9vvs ftp://data.pdbj.org/pub/pdb/validation_reports/vv/9vvs	HTTPS FTP

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Related structure data

Related structure data	9vw7C 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	#127 - Jul 2010 Crystallins similarity (1) #34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

B: Dehydrogenase

A: Dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: electron microscopy

Unit cell

Length a, b, c (Å)	117.710, 117.710, 98.987
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Dehydrogenase Mass: 31809.783 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
#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.69 Å³/Da / Density % sol: 54.36 %
Crystal grow	Temperature: 279.15 K / Method: vapor diffusion, hanging drop Details: 0.05 M Sodium acetate: Acetic acid pH 5.4, 0.8/1.2 M NaH2PO4/K2HPO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54184 Å
Detector	Type: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Apr 8, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2.68→12.716 Å / Num. all: 48016 / Num. obs: 24402 / % possible obs: 99.1 % / Redundancy: 2 % / B_iso Wilson estimate: 10.1 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.047 / R_pim(I) all: 0.047 / R_rim(I) all: 0.191 / Net I/σ(I): 12.7
Reflection shell	Resolution: 2.68→2.77 Å / R_merge(I) obs: 0.372 / Num. unique obs: 1927 / CC_1/2: 0.97 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
CrysalisPro		data reduction
Aimless		data scaling
MrBUMP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.68→12.716 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.838 / SU B: 11.118 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / ESU R: 0.97 / ESU R Free: 0.328
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2477	1009	5.081 %
R_work	0.1876	18850	-
all	0.191	-	-
obs	-	19859	98.816 %

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: 11.846 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.097 Å²	0 Å²	0 Å²
2-	-	1.097 Å²	0 Å²
3-	-	-	-2.195 Å²

Refinement step

Cycle: LAST / Resolution: 2.68→12.716 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4089	0	97	218	4404

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	4257
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4027
X-RAY DIFFRACTION	r_angle_refined_deg	1.351	1.635	5820
X-RAY DIFFRACTION	r_angle_other_deg	0.444	1.573	9207
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.658	5	569
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.758	5	37
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.105	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.875	10	607
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.024	10	157
X-RAY DIFFRACTION	r_chiral_restr	0.056	0.2	688
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5168
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	930
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	1000
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	3783
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2116
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2400
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	196
X-RAY DIFFRACTION	r_metal_ion_refined	0.205	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.167	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.169	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	1.238	1.201	2282
X-RAY DIFFRACTION	r_mcbond_other	1.237	1.201	2282
X-RAY DIFFRACTION	r_mcangle_it	2.188	2.155	2849
X-RAY DIFFRACTION	r_mcangle_other	2.188	2.155	2850
X-RAY DIFFRACTION	r_scbond_it	1.752	1.42	1975
X-RAY DIFFRACTION	r_scbond_other	1.752	1.423	1973
X-RAY DIFFRACTION	r_scangle_it	3.032	2.543	2971
X-RAY DIFFRACTION	r_scangle_other	3.031	2.546	2972
X-RAY DIFFRACTION	r_lrange_it	5.876	11.126	4839
X-RAY DIFFRACTION	r_lrange_other	5.939	11.131	4804

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
2.68-2.746	0.318	76	0.247	1319	0.251	1395	0.929	0.96	100	0.222
2.746-2.818	0.315	75	0.234	1272	0.238	1347	0.931	0.958	100	0.217
2.818-2.896	0.262	60	0.236	1269	0.237	1329	0.946	0.962	100	0.22
2.896-2.98	0.286	65	0.233	1215	0.236	1280	0.94	0.967	100	0.217
2.98-3.072	0.239	71	0.214	1191	0.216	1262	0.952	0.969	100	0.196
3.072-3.173	0.254	51	0.216	1154	0.218	1205	0.958	0.969	100	0.186
3.173-3.285	0.326	70	0.219	1123	0.225	1193	0.925	0.967	100	0.192
3.285-3.41	0.243	51	0.184	1084	0.187	1135	0.963	0.978	100	0.16
3.41-3.55	0.265	56	0.183	1053	0.187	1109	0.948	0.978	100	0.163
3.55-3.709	0.262	55	0.176	999	0.18	1054	0.953	0.978	100	0.159
3.709-3.891	0.237	60	0.166	943	0.17	1003	0.964	0.981	100	0.152
3.891-4.103	0.214	47	0.156	921	0.159	969	0.973	0.983	99.8968	0.142
4.103-4.354	0.218	43	0.149	880	0.152	923	0.968	0.985	100	0.136
4.354-4.658	0.24	43	0.156	820	0.16	863	0.966	0.984	100	0.146
4.658-5.035	0.182	37	0.139	768	0.14	805	0.98	0.989	100	0.129
5.035-5.522	0.229	32	0.166	732	0.168	764	0.964	0.985	100	0.152
5.522-6.185	0.214	37	0.168	645	0.17	682	0.975	0.983	100	0.153
6.185-7.163	0.222	30	0.12	574	0.124	604	0.968	0.991	100	0.113
7.163-8.826	0.13	28	0.137	499	0.137	527	0.99	0.991	100	0.134
8.826-12.716	0.146	22	0.173	390	0.172	415	0.993	0.992	99.2771	0.169

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