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- PDB-1n5d: CRYSTAL STRUCTURE OF PORCINE TESTICULAR CARBONYL REDUCTASE/ 20BET... -

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Basic information

Entry
Database: PDB / ID: 1n5d
TitleCRYSTAL STRUCTURE OF PORCINE TESTICULAR CARBONYL REDUCTASE/ 20BETA-HYDROXYSTEROID DEHYDROGENASE
ComponentsCARBONYL REDUCTASE/20BETA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / SHORTCHAIN DEHYDROGENASE/REDUCTASE / MONOMER / NADP-COMPLEX
Function / homology
Function and homology information


15-hydroxyprostaglandin-D dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) / alcohol dehydrogenase [NAD(P)+] / 15-hydroxyprostaglandin dehydrogenase (NADP+) activity / prostaglandin-E2 9-reductase / prostaglandin E2 9-reductase activity / S-nitrosoglutathione reductase (NADPH) activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity ...15-hydroxyprostaglandin-D dehydrogenase (NADP+) / 15-hydroxyprostaglandin dehydrogenase (NADP+) / alcohol dehydrogenase [NAD(P)+] / 15-hydroxyprostaglandin dehydrogenase (NADP+) activity / prostaglandin-E2 9-reductase / prostaglandin E2 9-reductase activity / S-nitrosoglutathione reductase (NADPH) activity / carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / 15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity / vitamin K metabolic process / xenobiotic metabolic process / lipid metabolic process / cytoplasm
Similarity search - Function
Carbonyl reductase [NADPH] 1-like / short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Carbonyl reductase [NADPH] 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsGhosh, D.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Porcine Carbonyl Reductase: Structural Basis for a Functional Monomer in Short-Chain Dehydrogenases/Reductases
Authors: Ghosh, D. / Sawicki, M. / Pletnev, V. / Erman, M. / Duax, W.L. / Ohno, S. / Nakajin, S.
#1: Journal: J.Steroid Biochem.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Diffraction Studies of a Mammalian Steroid Dehydrogenase
Authors: Ghosh, D. / Erman, M. / Pangborn, W. / Duax, W.L. / Nakajin, S. / Ohno, S. / Shinoda, M.
History
DepositionNov 5, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionNov 13, 2002ID: 1HU4
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CARBONYL REDUCTASE/20BETA-HYDROXYSTEROID DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4423
Polymers31,6001
Non-polymers8412
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.530, 58.530, 165.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CARBONYL REDUCTASE/20BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 31600.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: Q28960, 3alpha(or 20beta)-hydroxysteroid dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Method: other
Details: Ghosh, D., (1993) J. Steroid Biochem. Mol. Biol., 46, 103.

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 10, 1992 / Details: MONOCHROMATORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 10792 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 2 % / % possible all: 52
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 55.2 Å / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 25 Å2
Reflection shell
*PLUS
% possible obs: 52 % / Redundancy: 2 %

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Processing

Software
NameClassification
SCALEPACKdata scaling
PHASESphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.3→100 Å / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflectionSelection details
Rfree0.251 540 RANDOM
Rwork0.194 --
obs0.194 10792 -
Refine analyze
FreeObs
Luzzati sigma a0.37 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 53 58 2330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 55.2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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