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- PDB-2w4q: Crystal structure of human zinc-binding alcohol dehydrogenase 1 (... -

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Basic information

Entry
Database: PDB / ID: 2w4q
TitleCrystal structure of human zinc-binding alcohol dehydrogenase 1 (ZADH1) in ternary complex with NADP and 18beta-glycyrrhetinic acid
ComponentsPROSTAGLANDIN REDUCTASE 2
KeywordsOXIDOREDUCTASE / 15-OXOPROSTALGLANDIN / MEDIUM-CHAIN DEHYDROGENASE/REDUCTASE / NADP
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
Prostaglandin reductase 2 / Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Prostaglandin reductase 2 / Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CBW / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Prostaglandin reductase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShafqat, N. / Yue, W.W. / Ugochukwu, E. / Picaud, S. / Niesen, F. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of Human Zinc-Binding Alcohol Dehydrogenase 1
Authors: Shafqat, N. / Yue, W.W. / Niesen, F. / Oppermann, U.
History
DepositionNov 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 4, 2013Group: Non-polymer description / Refinement description / Source and taxonomy
Revision 1.3Dec 13, 2023Group: 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_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_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 ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROSTAGLANDIN REDUCTASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4018
Polymers39,3321
Non-polymers2,0697
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.374, 84.110, 72.888
Angle α, β, γ (deg.)90.00, 109.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROSTAGLANDIN REDUCTASE 2 / 15-OXOPROSTAGLANDIN 13-REDUCTASE / ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 1 / ...15-OXOPROSTAGLANDIN 13-REDUCTASE / ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 1 / PRG-2 / ZINC-BINDING ALCOHOL DEHYDROGENASE 1


Mass: 39331.707 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, 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
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CBW / (3BETA,5BETA,14BETA)-3-HYDROXY-11-OXOOLEAN-12-EN-29-OIC ACID


Mass: 470.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H46O4 / Comment: antiinflammatory*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 % / Description: NONE
Crystal growDetails: 0.1M TRIS PH 8.5; 2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Oct 29, 2008 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→68.9 Å / Num. obs: 25301 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0055refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VNA

2vna


Resolution: 2→68.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.072 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1341 5 %RANDOM
Rwork0.177 ---
obs0.18 25301 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.11 Å2
2--0.29 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2→68.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2652 0 136 187 2975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222873
X-RAY DIFFRACTIONr_bond_other_d0.0010.021883
X-RAY DIFFRACTIONr_angle_refined_deg1.4132.0153941
X-RAY DIFFRACTIONr_angle_other_deg0.8353.0054538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7675356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.28525.259116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14515469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6841511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213114
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02515
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.87831734
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.91352801
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.11871139
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.737111136
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 83
Rwork0.265 1817
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.82160.1077-0.57521.9164-0.45161.1745-0.1602-0.2089-0.10710.04380.0948-0.07010.18240.07770.06540.15370.06410.05390.17250.05020.03188.652-22.74230.466
22.3416-1.1984-0.59264.58070.03241.3116-0.1919-0.6860.11260.5780.2467-0.0530.0530.2272-0.05490.21690.08690.05310.34460.01130.03943.959-13.62138.987
31.3514-0.128-0.61420.97770.08931.39220.0788-0.00140.2506-0.08380.01350.0328-0.0776-0.0862-0.09220.11430.03670.04810.10450.00090.07138.4390.94414.493
42.1371-0.2399-0.90751.4432-0.2771.65670.00950.01420.1992-0.17970.0206-0.29190.09580.2945-0.03010.12170.03370.09460.15060.00810.108122.183-3.90910.078
51.04370.2804-0.1741.7784-0.50641.0806-0.02-0.06850.0738-0.03530.05930.21410.0939-0.1495-0.03930.08680.0170.03590.15020.01010.04972.13-7.71120.982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 68
2X-RAY DIFFRACTION2A69 - 118
3X-RAY DIFFRACTION3A119 - 208
4X-RAY DIFFRACTION4A209 - 297
5X-RAY DIFFRACTION5A298 - 346

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