PDB-2w98: CRYSTAL STRUCTURE OF HUMAN ZINC-BINDING ALCOHOL DEHYDROGENASE 1 (...

ID or keywords:

Entry

Database: PDB / ID: 2w98

Title

CRYSTAL STRUCTURE OF HUMAN ZINC-BINDING ALCOHOL DEHYDROGENASE 1 (ZADH1) IN TERNARY COMPLEX WITH NADP AND PHENYLBUTAZONE

Components

PROSTAGLANDIN REDUCTASE 2

Keywords

OXIDOREDUCTASE / 15-OXOPROSTALGLANDIN / MEDIUM-CHAIN DEHYDROGENASE/REDUCTASE

Function / homology

Function and homology information

13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-reductase [NAD(P)+] activity / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin metabolic process / cytoplasm
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Shafqat, N. / Yue, W.W. / Muniz, J. / Picaud, S. / Niesen, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.

Citation

Journal: To be Published
Title: Crystal Structure of Human Zinc-Binding Alcohol Dehydrogenase 1
Authors: Shafqat, N. / Yue, W.W. / Niesen, F. / Oppermann, U.

History

Deposition	Jan 22, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 7, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 4, 2013	Group: Non-polymer description / Source and taxonomy
Revision 1.3	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2w98.cif.gz	169.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2w98.ent.gz	133.5 KB	Display	PDB format
PDBx/mmJSON format	2w98.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2w98_validation.pdf.gz	3.2 MB	Display	wwPDB validaton report
Full document	2w98_full_validation.pdf.gz	3.2 MB	Display
Data in XML	2w98_validation.xml.gz	35.8 KB	Display
Data in CIF	2w98_validation.cif.gz	50.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w9/2w98 ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w98	HTTPS FTP

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Related structure data

Related structure data	2w4qC 2vnaS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2zb3-d 2y05-1 1h2s-d 4n03-d 2aqs-d 2f93-d 1po9-2 1jpd-d 6i94-d 2w4q-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#13 - Jan 2001 Alcohol Dehydrogenase similarity (3) #190 - Oct 2015 Two-component Systems similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #32 - Aug 2002 Chaperones similarity (1)

Deposited unit

A: PROSTAGLANDIN REDUCTASE 2

B: PROSTAGLANDIN REDUCTASE 2

hetero molecules

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

1

A: PROSTAGLANDIN REDUCTASE 2

hetero molecules

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

2

B: PROSTAGLANDIN REDUCTASE 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	141.014, 82.793, 69.097
Angle α, β, γ (deg.)	90.00, 99.77, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	ASP	ASP	3	A	A	1 - 59	2 - 60
2	1	MET	MET	ASP	ASP	3	B	B	1 - 59	2 - 60
1	2	THR	THR	ILE	ILE	6	A	A	60 - 65	61 - 66
2	2	THR	THR	ILE	ILE	6	B	B	60 - 65	61 - 66
1	3	THR	THR	HIS	HIS	3	A	A	66 - 149	67 - 150
2	3	THR	THR	HIS	HIS	3	B	B	66 - 149	67 - 150
1	4	ASN	ASN	SER	SER	2	A	A	155 - 346	156 - 347
2	4	ASN	ASN	SER	SER	2	B	B	155 - 346	156 - 347

NCS ensembles :

ID
1
2
3
4

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Protein , 1 types, 2 molecules AB

#1: Protein	PROSTAGLANDIN REDUCTASE 2 / PRG-2 / 15-OXOPROSTAGLANDIN 13-REDUCTASE / ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING ...PRG-2 / 15-OXOPROSTAGLANDIN 13-REDUCTASE / ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 1 / ZINC-BINDING ALCOHOL DEHYDROGENASE 1 Mass: 39331.707 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-349 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 References: UniProt: Q8N8N7, 13,14-dehydro-15-oxoprostaglandin 13-reductase

#1: Protein

PROSTAGLANDIN REDUCTASE 2 / PRG-2 / 15-OXOPROSTAGLANDIN 13-REDUCTASE / ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING ...

Mass: 39331.707 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HOMO SAPIENS (human) / Plasmid: PNIC-CTHF / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: Q8N8N7, 13,14-dehydro-15-oxoprostaglandin 13-reductase

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Non-polymers , 7 types, 510 molecules

#2: 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
#3: Chemical	ChemComp-P1Z / 4-BUTYL-1,2-DIPHENYL-PYRAZOLIDINE-3,5-DIONE Mass: 308.374 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₁₉H₂₀N₂O₂
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#5: Chemical	ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₅
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.43 % / Description: NONE
Crystal grow	Details: 2.1M NA(MALATE)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9789
Detector	Type: MARRESEARCH / Detector: CCD / Date: Aug 27, 2008
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 1.85→53.37 Å / Num. obs: 66348 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / R_merge(I) obs: 0.05 / Net I/σ(I): 13.6
Reflection shell	Resolution: 1.85→1.95 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.16 / Mean I/σ(I) obs: 5.2 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0055	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VNA

2vna

Resolution: 1.85→53.4 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.967 / SU B: 4.598 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.188	1319	2 %	RANDOM
R_work	0.158	-	-	-
obs	0.159	64962	99.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 8.15 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.53 Å²	0 Å²	1.14 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	0.82 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→53.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5382	0	293	493	6168

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	5906
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3913
X-RAY DIFFRACTION	r_angle_refined_deg	1.591	2.015	8045
X-RAY DIFFRACTION	r_angle_other_deg	0.895	3.005	9415
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.591	5	736
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.427	25.466	247
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.229	15	986
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.235	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.113	0.2	884
X-RAY DIFFRACTION	r_gen_planes_refined	0.015	0.021	6514
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1050
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.349	3	3523
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.541	5	5710
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.335	8	2383
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	6.681	11	2317
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	345	tight positional	0.04	0.05
1	2	B	345	tight positional	0.04	0.05
3	1	A	482	tight positional	0.06	0.05
3	2	B	482	tight positional	0.06	0.05
4	1	A	1121	tight positional	0.04	0.05
4	2	B	1121	tight positional	0.04	0.05
4	1	A	1281	medium positional	0.04	0.5
4	2	B	1281	medium positional	0.04	0.5
1	1	A	450	loose positional	0.04	5
1	2	B	450	loose positional	0.04	5
2	1	A	72	loose positional	0.88	5
2	2	B	72	loose positional	0.88	5
3	1	A	568	loose positional	0.05	5
3	2	B	568	loose positional	0.05	5
1	1	A	345	tight thermal	0.12	0.5
1	2	B	345	tight thermal	0.12	0.5
3	1	A	482	tight thermal	0.15	0.5
3	2	B	482	tight thermal	0.15	0.5
4	1	A	1121	tight thermal	0.13	0.5
4	2	B	1121	tight thermal	0.13	0.5
4	1	A	1281	medium thermal	0.1	2
4	2	B	1281	medium thermal	0.1	2
1	1	A	450	loose thermal	0.12	10
1	2	B	450	loose thermal	0.12	10
2	1	A	72	loose thermal	2.65	10
2	2	B	72	loose thermal	2.65	10
3	1	A	568	loose thermal	0.15	10
3	2	B	568	loose thermal	0.15	10

LS refinement shell

Resolution: 1.85→1.9 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.256	91
R_work	0.205	4457

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	2.4188	-1.3335	2.0836	1.6632	-1.1851	1.8895	0.114	-0.0621	-0.2472	-0.0358	0.0687	0.1222	0.1619	-0.048	-0.1827	0.2298	0.0032	-0.139	0.0792	0.0004	0.1572	23.7	-28.258	31.982
2	0.9223	-0.0957	0.6363	2.1197	0.1946	0.5152	-0.0043	0.0453	-0.042	-0.0597	0.0373	-0.2502	-0.023	0.0492	-0.033	0.1883	-0.0058	-0.1012	0.1086	-0.0109	0.1088	30.607	-14.699	32.371
3	0.9997	0.029	0.5937	0.7598	0.1785	0.9016	-0.0922	-0.1011	0.0994	0.027	-0.0071	0.0675	-0.157	-0.1325	0.0993	0.1997	0.0304	-0.127	0.125	-0.0233	0.1091	8.846	0.432	28.141
4	1.0027	-0.2954	0.4114	0.8106	-0.1162	0.838	-0.0098	0.0063	-0.0256	-0.0901	0.0083	0.1192	-0.029	-0.0884	0.0016	0.1917	0.0062	-0.1345	0.1161	-0.0104	0.0992	10.245	-5.409	21.427
5	2.25	1.1968	2.1471	1.5582	0.9215	2.1681	0.0511	0.0922	-0.1635	-0.0222	0.0751	-0.1015	0.1335	0.0736	-0.1262	0.2319	-0.0066	-0.1086	0.0884	-0.0146	0.1447	41.169	-29.683	1.635
6	0.8232	0.1984	0.4116	2.1386	-0.0952	0.376	-0.0554	0.0424	0	-0.042	0.0597	0.285	-0.0205	-0.0334	-0.0043	0.1805	-0.0025	-0.1115	0.1144	0.0051	0.1243	34.092	-16.126	1.503
7	1.2113	0.0059	0.4308	0.7882	-0.3488	0.9526	-0.1104	0.0741	0.0833	0.0331	0.0054	-0.1126	-0.2126	0.1028	0.1051	0.2176	-0.0248	-0.1323	0.1089	0.0103	0.1059	55.693	-0.29	6.336
8	0.9731	0.2612	0.2368	1.0671	-0.0611	0.8572	-0.0339	-0.0234	-0.0513	0.1568	0.0202	-0.1471	-0.0711	0.094	0.0137	0.2128	-0.0022	-0.1372	0.1146	0.0051	0.0953	54.379	-6.823	12.614

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 31
2	X-RAY DIFFRACTION	2	A	32 - 121
3	X-RAY DIFFRACTION	3	A	122 - 207
4	X-RAY DIFFRACTION	4	A	208 - 346
5	X-RAY DIFFRACTION	5	B	0 - 31
6	X-RAY DIFFRACTION	6	B	32 - 121
7	X-RAY DIFFRACTION	7	B	122 - 207
8	X-RAY DIFFRACTION	8	B	208 - 346

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Jul 12, 2017. Major update of PDB

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Yorodumi