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- PDB-1q5m: Binary complex of rabbit 20alpha-hydroxysteroid dehydrogenase wit... -

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Basic information

Entry
Database: PDB / ID: 1q5m
TitleBinary complex of rabbit 20alpha-hydroxysteroid dehydrogenase with NADPH
ComponentsProstaglandin-E2 9-reductase
KeywordsOXIDOREDUCTASE / NADPH / HSD / hydroxysteroid dehydrogenase / aldo-keto reductase
Function / homology
Function and homology information


prostaglandin-E2 9-reductase / prostaglandin-E2 9-reductase activity / 20alpha-hydroxysteroid dehydrogenase / 17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity / prostaglandin biosynthetic process / cytoplasm
Similarity search - Function
Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Prostaglandin-E(2) 9-reductase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsCouture, J.F. / Legrand, P. / Cantin, L. / Labrie, F. / Luu-The, V. / Breton, R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Loop Relaxation, A Mechanism that Explains the Reduced Specificity of Rabbit 20alpha-Hydroxysteroid Dehydrogenase, A Member of the Aldo-Keto Reductase Superfamily.
Authors: Couture, J.F. / Legrand, P. / Cantin, L. / Labrie, F. / Luu-The, V. / Breton, R.
History
DepositionAug 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Prostaglandin-E2 9-reductase
B: Prostaglandin-E2 9-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8616
Polymers73,1782
Non-polymers1,6834
Water13,205733
1
A: Prostaglandin-E2 9-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4313
Polymers36,5891
Non-polymers8412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prostaglandin-E2 9-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4313
Polymers36,5891
Non-polymers8412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.540, 85.270, 66.150
Angle α, β, γ (deg.)90.00, 91.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Prostaglandin-E2 9-reductase / / 20-alpha-hydroxysteroid dehydrogenase / 20-alpha-HSD


Mass: 36589.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3(pLysS)
References: UniProt: P80508, prostaglandin-E2 9-reductase, 20alpha-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: LiSO4 and PEG 4K, pH 7.5, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.32→57.74 Å / Num. obs: 141980 / Redundancy: 3.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.1
Reflection shellResolution: 1.32→1.37 Å / % possible all: 69.1

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→57.74 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.642 / SU ML: 0.031 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 5499 3.8 %RANDOM
Rwork0.1481 ---
all0.3206 ---
obs0.14918 138538 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.928 Å2
Refinement stepCycle: LAST / Resolution: 1.32→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5156 0 106 733 5995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0225436
X-RAY DIFFRACTIONr_bond_other_d0.0020.024879
X-RAY DIFFRACTIONr_angle_refined_deg2.6071.9777374
X-RAY DIFFRACTIONr_angle_other_deg1.427311436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0125642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.59215954
X-RAY DIFFRACTIONr_chiral_restr0.1810.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025882
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021058
X-RAY DIFFRACTIONr_nbd_refined0.280.21264
X-RAY DIFFRACTIONr_nbd_other0.2080.25201
X-RAY DIFFRACTIONr_nbtor_other0.0960.22995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.2494
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0920.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.222
X-RAY DIFFRACTIONr_mcbond_it1.8731.54104
X-RAY DIFFRACTIONr_mcangle_it2.07625229
X-RAY DIFFRACTIONr_scbond_it3.61432584
X-RAY DIFFRACTIONr_scangle_it4.6624.52145
LS refinement shellResolution: 1.32→1.366 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.244 564
Rwork0.214 10717
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.29360.8526-0.44451.1872-0.50991.15570.03180.02140.07150.07460.01250.0932-0.08640.0592-0.0443-0.0542-0.00350.0307-0.04990.0003-0.066616.2630.00232.157
20.89860.39260.17880.82010.2740.6556-0.0249-0.0083-0.0346-0.0294-0.0035-0.02850.0054-0.05290.0283-0.0458-0.00850.0217-0.0291-0.0173-0.075542.0540.92-0.121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 3231 - 322
2X-RAY DIFFRACTION1AC10011
3X-RAY DIFFRACTION1AE10031
4X-RAY DIFFRACTION1AG1004 - 13361 - 333
5X-RAY DIFFRACTION2BB2 - 3231 - 322
6X-RAY DIFFRACTION2BD10021
7X-RAY DIFFRACTION2BF10041
8X-RAY DIFFRACTION2BH1005 - 14041 - 400

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