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- PDB-2dkn: Crystal structure of the 3-alpha-hydroxysteroid dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 2dkn
TitleCrystal structure of the 3-alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831 complexed with NADH
Components3-alpha-hydroxysteroid dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


3alpha-hydroxysteroid 3-dehydrogenase (Si-specific) / oxidoreductase activity / nucleotide binding
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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 3-alpha-hydroxysteroid dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakamura, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Apo- and Holo-structures of 3{alpha}-Hydroxysteroid Dehydrogenase from Pseudomonas sp. B-0831: LOOP-HELIX TRANSITION INDUCED BY COENZYME BINDING
Authors: Nakamura, S. / Oda, M. / Kataoka, S. / Ueda, S. / Uchiyama, S. / Yoshida, T. / Kobayashi, Y. / Ohkubo, T.
History
DepositionApr 12, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: 3-alpha-hydroxysteroid dehydrogenase
B: 3-alpha-hydroxysteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4973
Polymers51,8312
Non-polymers6651
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-36 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.457, 82.248, 86.569
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 3-alpha-hydroxysteroid dehydrogenase


Mass: 25915.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: B-0831 / Plasmid: pUC118, pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1
References: UniProt: Q59718, 3alpha-hydroxysteroid 3-dehydrogenase (Si-specific)
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris/HCl (pH 9.0), 0.14M sodium chloride, 1.4M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 41776 / Num. obs: 41776 / % possible obs: 99.5 % / Redundancy: 7.38 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 24.56
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 5.8 / Num. unique all: 5826 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FK8

1fk8


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.233 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 2111 5.1 %RANDOM
Rwork0.17219 ---
all0.186 41776 --
obs0.17384 39665 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.703 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 44 376 3826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.9894754
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3815476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76523.386127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7415523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0821529
X-RAY DIFFRACTIONr_chiral_restr0.1080.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022627
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.31785
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.52465
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5550
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.357
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2630.549
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.20322414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82233706
X-RAY DIFFRACTIONr_scbond_it1.63321200
X-RAY DIFFRACTIONr_scangle_it2.5231048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 153 -
Rwork0.192 2864 -
obs--98.66 %

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