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- PDB-1hxh: COMAMONAS TESTOSTERONI 3BETA/17BETA HYDROXYSTEROID DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1hxh
TitleCOMAMONAS TESTOSTERONI 3BETA/17BETA HYDROXYSTEROID DEHYDROGENASE
Components3BETA/17BETA-HYDROXYSTEROID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / alpha-beta / Rossmann fold / short-chain dehydrogenase
Function / homology
Function and homology information


3(or 17)beta-hydroxysteroid dehydrogenase / testosterone dehydrogenase (NADP+) activity / testosterone dehydrogenase (NAD+) activity / steroid metabolic process
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
3-beta-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsBenach, J. / Filling, C. / Oppermann, U.C.T. / Roversi, P. / Bricogne, G. / Berndt, K.D. / Jornvall, H. / Ladenstein, R.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of Bacterial 3beta/17beta-Hydroxysteroid Dehydrogenase at 1.2 A Resolution: A Model for Multiple Steroid Recognition
Authors: Benach, J. / Filling, C. / Oppermann, U.C.T. / Roversi, P. / Bricogne, G. / Berndt, K.D. / Jornvall, H. / Ladenstein, R.
History
DepositionJan 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3BETA/17BETA-HYDROXYSTEROID DEHYDROGENASE
B: 3BETA/17BETA-HYDROXYSTEROID DEHYDROGENASE
C: 3BETA/17BETA-HYDROXYSTEROID DEHYDROGENASE
D: 3BETA/17BETA-HYDROXYSTEROID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)107,3914
Polymers107,3914
Non-polymers00
Water22,6271256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14980 Å2
ΔGint-85 kcal/mol
Surface area36130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.024, 110.595, 115.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
3BETA/17BETA-HYDROXYSTEROID DEHYDROGENASE


Mass: 26847.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: P19871, 3(or 17)beta-hydroxysteroid dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1256 / 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: 2.36 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% Ethanol, 250 mM NaCl, 50 mM Tris/HCl, 10 mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.9 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
310 mMdithiothreitol1drop
410 %ethanol1reservoir
5250 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8424 Å / Relative weight: 1
ReflectionResolution: 1.18→40 Å / Num. all: 1409412 / Num. obs: 1409412 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -1 / Redundancy: 4 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.22→1.25 Å / Rmerge(I) obs: 0.383 / % possible all: 83.9
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 314581 / Num. measured all: 1409412
Reflection shell
*PLUS
% possible obs: 83.9 % / Mean I/σ(I) obs: 54.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
CNSrefinement
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HSD

2hsd


Resolution: 1.22→20 Å / SU ML: 0.15 / Cross valid method: free / σ(F): 0 / σ(I): 0 / ESU R: 0.16 / ESU R Free: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.18 1839 0.6 %random
Rwork0.146 ---
obs-301844 96.6 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7854 0 0 1256 9110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.317
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
LS refinement shellResolution: 1.22→20 Å / Rfactor Rfree: 0.18 / Rfactor Rwork: 0.146
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.32
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23.9
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.172 / Rfactor Rwork: 0.139

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