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- PDB-2zb3: Crystal structure of mouse 15-ketoprostaglandin delta-13-reductas... -

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Basic information

Entry
Database: PDB / ID: 2zb3
TitleCrystal structure of mouse 15-ketoprostaglandin delta-13-reductase in complex with NADPH
ComponentsProstaglandin reductase 2
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / : / prostaglandin metabolic process / mitochondrion / cytosol
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
Chem-NDP / Prostaglandin reductase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
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)38,9442
Polymers38,1981
Non-polymers7451
Water8,359464
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)77,8874
Polymers76,3972
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_553-y,-x,-z-3/21
Buried area4950 Å2
ΔGint-17 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.829, 85.829, 100.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-401-

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: 38198.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptgr2, Zadh1 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8VDQ1, 13,14-dehydro-15-oxoprostaglandin 13-reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FEATURE OF UNIPROT (PTGR2_MOUSE, Q8VDQ1) SHOWS CONFLICT AT THIS POSITION: P -> T (IN REF. 1; BAB32284)

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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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M cacodylate, pH6.5, 27% PEG 8000, 80mM Mg(OAc)2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 13, 2004 / 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: 26149 / Num. obs: 24685 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2447 / % possible all: 96.1

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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 1V3V

1v3v


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
Rfree0.279 1119 -RANDOM
Rwork0.209 ---
all0.213 26103 --
obs0.213 23101 88.5 %-
Displacement parametersBiso mean: 33.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 48 464 3132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_bond_d0.02
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.35 94 -
Rwork0.318 --
obs-2101 82.4 %

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