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- PDB-8kcz: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhod... -

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Basic information

Entry
Database: PDB / ID: 8kcz
TitleCrystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
Components3-ketosteroid dehydrogenase
KeywordsOXIDOREDUCTASE / 3-ketosteroid delta1-dehydrogenase / Rhodococcus erythropolis SQ1 / 1 / 4-androstadiene-3 / 17- dione
Function / homology
Function and homology information


3-oxosteroid 1-dehydrogenase / 3-oxosteroid 1-dehydrogenase activity / steroid metabolic process / nucleotide binding
Similarity search - Function
: / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ANDROSTA-1,4-DIENE-3,17-DIONE / FLAVIN-ADENINE DINUCLEOTIDE / 3-oxosteroid 1-dehydrogenase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHu, Y.L. / Li, X. / Cheng, X.Y. / Song, S.K. / Su, Z.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione
Authors: Song, S.K. / Su, Z.D.
History
DepositionAug 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-ketosteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7213
Polymers54,6511
Non-polymers1,0702
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.890, 118.890, 118.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein 3-ketosteroid dehydrogenase / 3-oxosteroid 1-dehydrogenase


Mass: 54651.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: kstD1, BS297_24040, rerp_49010, RERY_47440 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RA02, 3-oxosteroid 1-dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ANB / ANDROSTA-1,4-DIENE-3,17-DIONE


Mass: 284.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H24O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.43 Å3/Da / Density % sol: 72.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1M BIS-TRIS ph 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→102.96 Å / Num. obs: 42673 / % possible obs: 99.7 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.019 / Net I/σ(I): 19.3
Reflection shellResolution: 2.34→2.47 Å / Rmerge(I) obs: 1.292 / Num. unique obs: 5911

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22291 2164 5.1 %RANDOM
Rwork0.19166 ---
obs0.19324 40509 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.403 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.59 Å2-0 Å2
2--1.17 Å20 Å2
3----3.8 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 74 4 3920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134000
X-RAY DIFFRACTIONr_bond_other_d0.0370.0173588
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.6415450
X-RAY DIFFRACTIONr_angle_other_deg2.4591.5748314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84622.304204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74115581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1291528
X-RAY DIFFRACTIONr_chiral_restr0.0930.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024666
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02835
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6885.5312091
X-RAY DIFFRACTIONr_mcbond_other4.6695.5282090
X-RAY DIFFRACTIONr_mcangle_it5.9758.2922612
X-RAY DIFFRACTIONr_mcangle_other5.9748.2952613
X-RAY DIFFRACTIONr_scbond_it6.6236.0241909
X-RAY DIFFRACTIONr_scbond_other6.6226.0231910
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.0338.8052839
X-RAY DIFFRACTIONr_long_range_B_refined13.36965.0854245
X-RAY DIFFRACTIONr_long_range_B_other13.36865.0864246
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 167 -
Rwork0.286 2930 -
obs--100 %

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