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- PDB-1fk8: THE CRYSTAL STRUCTURE OF THE BINARY COMPLEX WITH NAD OF 3-ALPHA-H... -

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Basic information

Entry
Database: PDB / ID: 1fk8
TitleTHE CRYSTAL STRUCTURE OF THE BINARY COMPLEX WITH NAD OF 3-ALPHA-HYDROXYSTEROID DEHYDROGENASE FROM COMAMONAS TESTOSTERONI, A MEMBER OF THE SHORT CHAIN DEHYDROGENASE/REDUCTASE FAMILY
Components3ALPHA-HYDROXYSTEROID DEHYDROGENASE/CARBONYL REDUCTASE
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase / SDR / Carbonyl Reductase / Steroid / Hydroxysteroid / Xenobiotic / Metyrapone / Oligomerisation / Comamonas testosteroni / NAD / Nicotinamide Adenine Dinucleotide / substrate binding loop
Function / homology
Function and homology information


3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / androsterone dehydrogenase (B-specific) activity / nucleotide binding / cytoplasm
Similarity search - Function
short chain dehydrogenase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase / 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsGrimm, C. / Ficner, R. / Maser, E. / Klebe, G. / Reuter, K.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of 3alpha -hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family.
Authors: Grimm, C. / Maser, E. / Mobus, E. / Klebe, G. / Reuter, K. / Ficner, R.
History
DepositionAug 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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: 3ALPHA-HYDROXYSTEROID DEHYDROGENASE/CARBONYL REDUCTASE
B: 3ALPHA-HYDROXYSTEROID DEHYDROGENASE/CARBONYL REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1684
Polymers52,8412
Non-polymers1,3272
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-42 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.785, 46.195, 64.982
Angle α, β, γ (deg.)107.52, 106.34, 97.63
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a dimer constructed from chain A by the two-fold NCS axis.

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Components

#1: Protein 3ALPHA-HYDROXYSTEROID DEHYDROGENASE/CARBONYL REDUCTASE / HYDROXYSTEROID SHORT CHAIN DEHYDROGENASE/REDUCTASE / 3ALPHA-HSD/CR


Mass: 26420.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Comamonas testosteroni (bacteria)
References: UniProt: Q9ZFY9, UniProt: P80702*PLUS, 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG4000, ammonium acetate, cacodylate , NAD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5 / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 %PEG40001reservoir
20.1 Mcacodylate1reservoir
30.2 Mammonium acetate1reservoir
45 g/lprotein1drop
510 mMTris-HCl1drop
60.1 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→33.4 Å / Num. all: 30053 / Num. obs: 233945 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 25.7
Reflection shellResolution: 1.95→1.97 Å / Rmerge(I) obs: 0.275 / % possible all: 90.5
Reflection
*PLUS
Num. obs: 30053 / Num. measured all: 233945
Reflection shell
*PLUS
% possible obs: 90.5 %

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.95→33.4 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 260280.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 915 3 %RANDOM
Rwork0.185 ---
obs0.185 30053 93.2 %-
all-0 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.65 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20.38 Å20.11 Å2
2--0.75 Å20.94 Å2
3----1.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.95→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 88 358 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 150 3.2 %
Rwork0.221 4562 -
obs--88.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMNAD.TOP
X-RAY DIFFRACTION3NAD.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.25 / % reflection Rfree: 3.2 % / Rfactor Rwork: 0.221

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