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- PDB-1v3u: Crystal structure of leukotriene B4 12-hydroxydehydrogenase/15-ox... -

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Basic information

Entry
Database: PDB / ID: 1v3u
TitleCrystal structure of leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase in apo form
Componentsleukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase
KeywordsOXIDOREDUCTASE / Rossmann fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


2-alkenal reductase (NADPH) activity / leukotriene B4 metabolic process / 13-lipoxin reductase activity / leukotriene B4 12-hydroxy dehydrogenase activity / lipoxin A4 metabolic process / 2-alkenal reductase [NAD(P)+] / 13,14-dehydro-15-oxoprostaglandin 13-reductase / 13-prostaglandin reductase activity / 15-oxoprostaglandin 13-oxidase activity / prostaglandin metabolic process / cytoplasm
Similarity search - Function
Leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase / 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 / Polyketide synthase, enoylreductase domain / Enoylreductase ...Leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase / 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 / Polyketide synthase, enoylreductase domain / Enoylreductase / 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
Prostaglandin reductase 1
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHori, T. / Yokomizo, T. / Ago, H. / Sugahara, M. / Ueno, G. / Yamamoto, M. / Kumasaka, T. / Shimizu, T. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop
Authors: Hori, T. / Yokomizo, T. / Ago, H. / Sugahara, M. / Ueno, G. / Yamamoto, M. / Kumasaka, T. / Shimizu, T. / Miyano, M.
History
DepositionNov 5, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase
B: leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7129
Polymers72,4642
Non-polymers2487
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-95 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.486, 74.591, 79.296
Angle α, β, γ (deg.)90.00, 102.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase / leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase


Mass: 36231.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9EQZ5, 13,14-dehydro-15-oxoprostaglandin 13-reductase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.11 Å3/Da / Density % sol: 41.14 %
Crystal growTemperature: 291 K / Method: batch / pH: 6.5
Details: PEG 4000, MES, magnesium chloride, pH 6.5, batch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→32.2 Å / Num. all: 215877 / Num. obs: 45444 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 31.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 14.5 / Num. unique all: 4459 / % possible all: 98.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→32.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2306 -RANDOM
Rwork0.214 ---
all-42751 --
obs-42751 94.6 %-
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→32.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4982 0 7 748 5737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008629
X-RAY DIFFRACTIONc_angle_deg1.39012
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.3 219 -
Rwork0.24 --
obs-4265 94.9 %

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