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- PDB-2dm6: Crystal structure of anti-configuration of indomethacin and leuko... -

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Entry
Database: PDB / ID: 2dm6
TitleCrystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex
ComponentsNADP-dependent leukotriene B4 12-hydroxydehydrogenase
KeywordsOXIDOREDUCTASE / NAD(P)-binding Rossmann-fold domains / 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
INDOMETHACIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Prostaglandin reductase 1
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHori, T. / Ishijima, J. / Yokomizo, T. / Ago, H. / Shimizu, T. / Miyano, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem.(Tokyo) / Year: 2006
Title: Crystal structure of anti-configuration of indomethacin and leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase complex reveals the structural basis of broad spectrum indomethacin efficacy
Authors: Hori, T. / Ishijima, J. / Yokomizo, T. / Ago, H. / Shimizu, T. / Miyano, M.
History
DepositionApr 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
B: NADP-dependent leukotriene B4 12-hydroxydehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4726
Polymers72,4642
Non-polymers2,0084
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-42 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.253, 76.075, 79.646
Angle α, β, γ (deg.)90.00, 102.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NADP-dependent leukotriene B4 12-hydroxydehydrogenase / dehydrogenase/reductase / LTB4 / 12-HD / 15-oxoprostaglandin 13-reductase / PGR


Mass: 36231.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9EQZ5, 2-alkenal reductase [NAD(P)+], 13,14-dehydro-15-oxoprostaglandin 13-reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-IMN / INDOMETHACIN / Indometacin


Mass: 357.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16ClNO4 / Comment: medication, antiinflammatory*YM
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 298 K / Method: oil batch / pH: 6.4
Details: 20% PEG 4000, 50mM magnesium chloride, 0.1M MES, pH 6.4, oil batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Apr 7, 2004
RadiationMonochromator: Diamond crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 45006 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07 / Χ2: 1.624 / Net I/σ(I): 51.9
Reflection shellResolution: 2→2.07 Å / % possible obs: 84.1 % / Rmerge(I) obs: 0.179 / Num. unique obs: 3844 / Χ2: 1.155 / % possible all: 84.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→34.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.451 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2216 4.9 %RANDOM
Rwork0.181 ---
all0.183 45006 --
obs-44983 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.06 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.04 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5079 0 132 600 5811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225327
X-RAY DIFFRACTIONr_angle_refined_deg1.1152.0067213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07524.949198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86115927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6341516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023897
X-RAY DIFFRACTIONr_nbd_refined0.1840.22557
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2509
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.246
X-RAY DIFFRACTIONr_mcbond_it2.0861.53401
X-RAY DIFFRACTIONr_mcangle_it2.74725266
X-RAY DIFFRACTIONr_scbond_it4.35232232
X-RAY DIFFRACTIONr_scangle_it6.2254.51947
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 153 -
Rwork0.203 2589 -
obs-2742 81.51 %
Refinement TLS params.Method: refined / Origin x: -5.4661 Å / Origin y: 68.0649 Å / Origin z: 8.8792 Å
111213212223313233
T0.0443 Å2-0.0331 Å20.0174 Å2-0.0517 Å20.0252 Å2--0.0679 Å2
L0.3106 °2-0.0599 °20.4233 °2-0.0634 °2-0.021 °2--0.6479 °2
S0.0009 Å °0.0114 Å °-0.021 Å °0.0328 Å °0.0192 Å °0.0218 Å °0.0126 Å °-0.0227 Å °-0.0201 Å °
Refinement TLS groupSelection: ALL

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