PDB-9knp: X-ray structure of Pyrococcus horikoshii OT3 alcohol dehydrogenase

ID or keywords:

Entry

Database: PDB / ID: 9knp

Title

X-ray structure of Pyrococcus horikoshii OT3 alcohol dehydrogenase

Components

375aa long hypothetical alchol dehydrogenase

Keywords

METAL BINDING PROTEIN / group 3 alcohol dehydrogenase / NAD

Function / homology

Function and homology information

alcohol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function

Biological species

Pyrococcus horikoshii OT3 (archaea)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.94 Å

Authors

Kamitori, S. / Nakamura, N.

Funding support

Japan, 1items

Citation

Journal: To Be Published
Title: X-ray structure of Pyrococcus horikoshii OT3 alcohol dehydrogenase
Authors: Kamitori, S. / Nakamura, N.

History

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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9knp.cif.gz	277.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9knp.ent.gz	216.9 KB	Display	PDB format
PDBx/mmJSON format	9knp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9knp_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	9knp_full_validation.pdf.gz	2.4 MB	Display
Data in XML	9knp_validation.xml.gz	38.2 KB	Display
Data in CIF	9knp_validation.cif.gz	52.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kn/9knp ftp://data.pdbj.org/pub/pdb/validation_reports/kn/9knp	HTTPS FTP

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Related structure data

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

Deposited unit

A: 375aa long hypothetical alchol dehydrogenase

B: 375aa long hypothetical alchol dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	68.890, 75.580, 166.500
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	375aa long hypothetical alchol dehydrogenase Mass: 42480.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: PH0743 / Production host: Escherichia coli (E. coli) / References: UniProt: O58517
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical	ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.55 Å³/Da / Density % sol: 51.78 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 200 mM potassium phosphate, 29% w/v polyethylene glycol 3350, 3 mM NAD+, 10 mM NiCl2, 2% v/v butanol, pH 4.9

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.94→19.5 Å / Num. obs: 63980 / % possible obs: 98.2 % / Redundancy: 6.8 % / CC_1/2: 0.99 / Net I/σ(I): 20.3
Reflection shell	Resolution: 1.94→1.99 Å / Num. unique obs: 4646 / CC_1/2: 0.92

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: An initial model was generated by PHYRE2 Server

Resolution: 1.94→19.497 Å / Cor.coef. F_o:F_c: 0.902 / Cor.coef. F_o:F_c free: 0.881 / SU B: 7.234 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.163
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2526	3170	4.955 %
R_work	0.2184	60810	-
all	0.22	-	-
obs	-	63980	98.192 %

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: 21.441 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.23 Å²	0 Å²	-0 Å²
2-	-	-0.114 Å²	0 Å²
3-	-	-	0.344 Å²

Refinement step

Cycle: LAST / Resolution: 1.94→19.497 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5836	0	100	458	6394

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	6056
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.015	5860
X-RAY DIFFRACTION	r_angle_refined_deg	1.284	1.645	8201
X-RAY DIFFRACTION	r_angle_other_deg	1.253	1.578	13580
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.168	5	749
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.633	23.127	275
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.181	15	1077
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.004	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	807
X-RAY DIFFRACTION	r_gen_planes_refined	0.016	0.02	6691
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1237
X-RAY DIFFRACTION	r_nbd_refined	0.204	2	1314
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	2	5352
X-RAY DIFFRACTION	r_nbtor_refined	0.153	0.2	2999
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	2640
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.094	0.2	422
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.059	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.268	2	26
X-RAY DIFFRACTION	r_nbd_other	0.213	2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.08	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.49	1.679	3002
X-RAY DIFFRACTION	r_mcbond_other	1.486	1.677	3001
X-RAY DIFFRACTION	r_mcangle_it	2.242	2.511	3749
X-RAY DIFFRACTION	r_mcangle_other	2.243	2.512	3750
X-RAY DIFFRACTION	r_scbond_it	2.742	2.065	3054
X-RAY DIFFRACTION	r_scbond_other	2.741	2.066	3055
X-RAY DIFFRACTION	r_scangle_it	3.593	2.965	4452
X-RAY DIFFRACTION	r_scangle_other	3.592	2.966	4453
X-RAY DIFFRACTION	r_lrange_it	5.395	21.693	6891
X-RAY DIFFRACTION	r_lrange_other	5.26	21.398	6796

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 (%)
1.94-1.99	0.306	248	0.253	4398	X-RAY DIFFRACTION	98.3697
1.99-2.045	0.253	230	0.188	4441	X-RAY DIFFRACTION	100
2.045-2.104	0.241	238	0.189	4247	X-RAY DIFFRACTION	100
2.104-2.169	0.213	207	0.188	4168	X-RAY DIFFRACTION	100
2.169-2.24	0.448	184	0.406	3574	X-RAY DIFFRACTION	88.4027
2.24-2.318	0.605	168	0.575	3491	X-RAY DIFFRACTION	88.7891
2.318-2.406	0.219	208	0.175	3772	X-RAY DIFFRACTION	100
2.406-2.504	0.243	184	0.171	3671	X-RAY DIFFRACTION	100
2.504-2.615	0.201	180	0.159	3497	X-RAY DIFFRACTION	99.9728
2.615-2.743	0.2	171	0.166	3333	X-RAY DIFFRACTION	99.9715
2.743-2.891	0.251	178	0.172	3186	X-RAY DIFFRACTION	99.9406
2.891-3.066	0.224	175	0.178	3011	X-RAY DIFFRACTION	99.9373
3.066-3.278	0.202	139	0.178	2897	X-RAY DIFFRACTION	99.8356
3.278-3.54	0.214	136	0.188	2645	X-RAY DIFFRACTION	99.8564
3.54-3.877	0.285	118	0.274	2464	X-RAY DIFFRACTION	99.2695
3.877-4.333	0.155	109	0.149	2229	X-RAY DIFFRACTION	99.1098
4.333-5.001	0.154	101	0.147	2007	X-RAY DIFFRACTION	99.9526
5.001-6.12	0.239	88	0.191	1702	X-RAY DIFFRACTION	99.9442
6.12-8.632	0.222	81	0.175	1343	X-RAY DIFFRACTION	100
8.632-19.4	0.181	27	0.184	734	X-RAY DIFFRACTION	89.5294

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	0.4171	-0.0339	-0.1071	0.0124	-0.0381	0.3905	0.0017	0.0248	0.0418	0.0021	-0.0207	-0.0106	-0.0284	0.0148	0.019	0.0297	-0.0016	0.0013	0.0476	0.0142	0.0097	22.5385	48.2942	52.399
2	0.4867	-0.3047	-0.0747	0.4341	-0.0068	0.1148	0.0458	-0.0204	0.0427	0.0473	-0.0311	0.0337	0.0208	0.0181	-0.0147	0.0498	-0.0112	0.0234	0.0138	-0.015	0.0201	10.8707	50.4748	74.1262
3	0.5498	-0.0085	0.2062	0.0659	0.1093	0.2742	0.0124	0.0654	-0.0399	0.0166	-0.0096	0.0053	0.0248	-0.0016	-0.0028	0.0321	-0.0017	0.0012	0.0412	-0.0148	0.006	11.8411	15.4269	51.6302
4	0.4773	-0.0801	-0.0021	0.2974	0.2341	0.2096	0.0058	-0.0229	-0.0526	0.0911	0.0061	-0.0124	0.0481	0.0121	-0.0119	0.0787	-0.0061	-0.0142	0.0296	0.0135	0.0121	23.2051	12.4115	73.1267

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 183
2	X-RAY DIFFRACTION	2	ALL	A	184 - 376
3	X-RAY DIFFRACTION	3	ALL	B	1 - 183
4	X-RAY DIFFRACTION	4	ALL	B	184 - 375

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