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- PDB-2zb8: Crystal structure of human 15-ketoprostaglandin delta-13-reductas... -

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Basic information

Entry
Database: PDB / ID: 2zb8
TitleCrystal structure of human 15-ketoprostaglandin delta-13-reductase in complex with NADP and indomethacin
ComponentsProstaglandin reductase 2
KeywordsOXIDOREDUCTASE / Rossmann fold / Alternative splicing / Cytoplasm / NADP
Function / homology
Function and homology information


13,14-dehydro-15-oxoprostaglandin 13-reductase / 13-prostaglandin reductase activity / 15-oxoprostaglandin 13-oxidase activity / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / prostaglandin metabolic process / cytoplasm
Similarity search - Function
Prostaglandin reductase 2 / Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / 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 / Medium-chain dehydrogenase/reductase / Oxidoreductase, N-terminal domain / 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
INDOMETHACIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Prostaglandin reductase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWu, Y.H. / Wang, A.H.J. / Ko, T.P. / Guo, R.T. / Hu, S.M. / Chuang, L.M.
CitationJournal: Structure / Year: 2008
Title: Structural basis for catalytic and inhibitory mechanisms of human prostaglandin reductase PTGR2.
Authors: Wu, Y.H. / Ko, T.P. / Guo, R.T. / Hu, S.M. / Chuang, L.M. / Wang, A.H.J.
History
DepositionOct 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prostaglandin reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2555
Polymers38,9611
Non-polymers1,2934
Water8,611478
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Prostaglandin reductase 2
hetero molecules

A: Prostaglandin reductase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,50910
Polymers77,9232
Non-polymers2,5878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area5910 Å2
ΔGint-99 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.482, 84.079, 73.318
Angle α, β, γ (deg.)90.00, 109.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1322-

HOH

21A-1348-

HOH

31A-1393-

HOH

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Components

#1: Protein Prostaglandin reductase 2 / PTGR2 / 15-oxoprostaglandin 13-reductase / Zinc-binding alcohol dehydrogenase domain-containing protein 1


Mass: 38961.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTGR2, ZADH1 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8N8N7, 13,14-dehydro-15-oxoprostaglandin 13-reductase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-IMN / INDOMETHACIN / Indometacin


Mass: 357.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication, antiinflammatory*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 51.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1M MES, pH 5.9, 2.0M ammonium sulfate, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2006 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 26604 / Num. obs: 26205 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 24.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2591 / % possible all: 98.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZB4

2zb4


Resolution: 2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1217 -RANDOM
Rwork0.171 ---
all0.173 26508 --
obs-25124 94.8 %-
Displacement parametersBiso mean: 46.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 83 478 3189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.77
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.005
RfactorNum. reflection% reflection
Rfree0.27 104 -
Rwork0.249 --
obs-2250 85.5 %

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