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- PDB-7zej: Crystal structure of the human MGC45594 gene product in complex w... -

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Basic information

Entry
Database: PDB / ID: 7zej
TitleCrystal structure of the human MGC45594 gene product in complex with celecoxib.
ComponentsProstaglandin reductase 3
KeywordsOXIDOREDUCTASE / alkenal reductases / prostaglandin reductases / phase 1 xenobiotic metabolism / reactive oxygen species / lipid peroxidation / polyunsaturated fatty acid / inflammation / lipid mediator metabolism / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


13,14-dehydro-15-oxoprostaglandin 13-reductase / 15-oxoprostaglandin 13-oxidase [NAD(P)+] activity / : / negative regulation of fat cell differentiation / peroxisome / mitochondrion / zinc ion binding
Similarity search - Function
Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-CEL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Prostaglandin reductase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsShafqat, N. / Yue, W.W. / Koekemoer, L. / Niesen, F. / Ugochukwu, E. / Vollmar, M. / Weigelt, J. / Krojer, T. / Pike, A. / Chaikaud, A. ...Shafqat, N. / Yue, W.W. / Koekemoer, L. / Niesen, F. / Ugochukwu, E. / Vollmar, M. / Weigelt, J. / Krojer, T. / Pike, A. / Chaikaud, A. / Von Delft, F. / Arrowsmith, C. / Bountra, C. / Edwards, A. / Opperman, U. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
The Structural Genomics Consortium (SGC) Canada
CitationJournal: To Be Published
Title: Human prostaglandin/alkenal reductases: substrate specificities, inhibitor profiles, structural insights and subcellular localization suggest protective roles in inflammatory and oxidative stress conditions.
Authors: Shafqat, N. / Dakin, S.G. / Estrada, F.M. / Niesen, F.H. / Wells, G. / Yapp, C. / Troumpra, M.K. / Brotherton, D. / Porte, S. / Mesa, J. / Yakovtseva, E. / Farres, J. / Pares, X. / Liu, T. / ...Authors: Shafqat, N. / Dakin, S.G. / Estrada, F.M. / Niesen, F.H. / Wells, G. / Yapp, C. / Troumpra, M.K. / Brotherton, D. / Porte, S. / Mesa, J. / Yakovtseva, E. / Farres, J. / Pares, X. / Liu, T. / Altman, R. / Carr, A. / Koekemoer, L. / Niesen, F. / Yue, W.W. / Opperman, U.
History
DepositionMar 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prostaglandin reductase 3
B: Prostaglandin reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7516
Polymers72,5012
Non-polymers2,2504
Water3,045169
1
A: Prostaglandin reductase 3
hetero molecules

B: Prostaglandin reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7516
Polymers72,5012
Non-polymers2,2504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6990 Å2
ΔGint-20 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.830, 51.410, 75.880
Angle α, β, γ (deg.)93.860, 91.480, 101.290
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Prostaglandin reductase 3 / PRG-3 / Zinc-binding alcohol dehydrogenase domain-containing protein 2


Mass: 36250.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZADH2, PTGR3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N4Q0, 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.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CEL / 4-[5-(4-METHYLPHENYL)-3-(TRIFLUOROMETHYL)-1H-PYRAZOL-1-YL]BENZENESULFONAMIDE / CELECOXIB


Mass: 381.372 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H14F3N3O2S / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.5M NA MALONATE pH 7.0, 0.25W/V JEFFAMINE ED 2001 pH 7.0 HEPES pH 8.0
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→16.76 Å / Num. obs: 101296 / % possible obs: 85.8 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 8.3
Reflection shellResolution: 1.79→1.89 Å / Rmerge(I) obs: 0.226 / Num. unique obs: 6992

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C0C

2c0c


Resolution: 1.79→16.76 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.935 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2337 1731 3.095 %
Rwork0.1847 54203 -
all0.186 --
obs-55934 85.782 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.314 Å2
Baniso -1Baniso -2Baniso -3
1--1.469 Å2-1.735 Å20.488 Å2
2--4.797 Å20.202 Å2
3----3.05 Å2
Refinement stepCycle: LAST / Resolution: 1.79→16.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 148 169 5391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135342
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155102
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6617276
X-RAY DIFFRACTIONr_angle_other_deg1.3191.57911769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34122.488201
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg8.439102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75415864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6341522
X-RAY DIFFRACTIONr_chiral_restr0.070.2698
X-RAY DIFFRACTIONr_chiral_restr_other1.9890.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021099
X-RAY DIFFRACTIONr_nbd_refined0.1990.2939
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.24563
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22597
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2215
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0720.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3020.217
X-RAY DIFFRACTIONr_nbd_other0.2070.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2940.28
X-RAY DIFFRACTIONr_mcbond_it1.9112.7242727
X-RAY DIFFRACTIONr_mcbond_other1.9112.7232726
X-RAY DIFFRACTIONr_mcangle_it2.9094.0763407
X-RAY DIFFRACTIONr_mcangle_other2.9084.0773408
X-RAY DIFFRACTIONr_scbond_it2.543.062615
X-RAY DIFFRACTIONr_scbond_other2.543.0622616
X-RAY DIFFRACTIONr_scangle_it3.9884.493869
X-RAY DIFFRACTIONr_scangle_other3.9884.4923870
X-RAY DIFFRACTIONr_lrange_it5.63932.7315627
X-RAY DIFFRACTIONr_lrange_other5.63432.7115610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.8360.3181000.3133164X-RAY DIFFRACTION67.9292
1.836-1.8870.321890.2973634X-RAY DIFFRACTION78.3624
1.887-1.9410.2811190.2753559X-RAY DIFFRACTION81.4257
1.941-2.0010.2871070.2453732X-RAY DIFFRACTION85.6728
2.001-2.0670.2771020.2363573X-RAY DIFFRACTION86.1463
2.067-2.1390.2391110.2233478X-RAY DIFFRACTION85.7792
2.139-2.220.2441190.1973401X-RAY DIFFRACTION87.1072
2.22-2.310.2341090.1893302X-RAY DIFFRACTION88.5514
2.31-2.4130.2681150.1773164X-RAY DIFFRACTION89.4679
2.413-2.5310.211110.1653102X-RAY DIFFRACTION90.3543
2.531-2.6670.2161000.1612958X-RAY DIFFRACTION90.9578
2.667-2.8290.264870.1762833X-RAY DIFFRACTION90.9374
2.829-3.0240.235710.1692633X-RAY DIFFRACTION90.314
3.024-3.2660.203830.1552437X-RAY DIFFRACTION90.3874
3.266-3.5770.214760.1662213X-RAY DIFFRACTION89.589
3.577-3.9980.191620.1632013X-RAY DIFFRACTION88.5617
3.998-4.6140.182610.1371659X-RAY DIFFRACTION84.8963
4.614-5.6460.278530.1631486X-RAY DIFFRACTION88.7032
5.646-7.9630.209390.1711245X-RAY DIFFRACTION96.5414
7.963-7.9630.217170.17617X-RAY DIFFRACTION85.3298

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