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

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Basic information

Entry
Database: PDB / ID: 8jbz
TitleCrystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 4-androstadiene-3,17- dione
Components3-ketosteroid dehydrogenase
KeywordsOXIDOREDUCTASE / 3-ketosteroid delta1-dehydrogenase / Rhodococcus erythropolis SQ1 / 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
: / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
4-ANDROSTENE-3-17-DIONE / FLAVIN-ADENINE DINUCLEOTIDE / 3-ketosteroid dehydrogenase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.079 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 4-androstadiene-3,17- dione
Authors: Hu, Y.L. / Li, X. / Cheng, X.Y. / Song, S.K. / Su, Z.D.
History
DepositionMay 10, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: 3-ketosteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3263
Polymers54,2541
Non-polymers1,0722
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-9 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.108, 120.108, 117.242
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11AAA-718-

HOH

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Components

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


Mass: 54253.914 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-ASD / 4-ANDROSTENE-3-17-DIONE


Mass: 286.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 4.5 Å3/Da / Density % sol: 72.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic, pH7.0

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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: 2.079→104.234 Å / Num. obs: 58119 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 1 / Net I/σ(I): 16.2
Reflection shellResolution: 2.08→2.14 Å / Num. unique obs: 4463 / CC1/2: 0.858

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.079→104.234 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2286 2850 4.904 %
Rwork0.1944 55264 -
all0.196 --
obs-58114 99.923 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 41.679 Å2
Baniso -1Baniso -2Baniso -3
1-0.813 Å20.407 Å20 Å2
2--0.813 Å2-0 Å2
3----2.637 Å2
Refinement stepCycle: LAST / Resolution: 2.079→104.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3812 0 74 105 3991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133970
X-RAY DIFFRACTIONr_bond_other_d0.0370.0173561
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.645408
X-RAY DIFFRACTIONr_angle_other_deg2.4421.5758253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66222.15200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64515575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1731528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024627
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02826
X-RAY DIFFRACTIONr_nbd_refined0.2140.2778
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.23320
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21996
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2129
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3910.212
X-RAY DIFFRACTIONr_nbd_other0.4090.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.21
X-RAY DIFFRACTIONr_mcbond_it3.6654.3182083
X-RAY DIFFRACTIONr_mcbond_other3.6654.3162082
X-RAY DIFFRACTIONr_mcangle_it4.7286.4622602
X-RAY DIFFRACTIONr_mcangle_other4.7276.4642603
X-RAY DIFFRACTIONr_scbond_it5.8014.6791887
X-RAY DIFFRACTIONr_scbond_other5.84.6791888
X-RAY DIFFRACTIONr_scangle_it7.7356.8442806
X-RAY DIFFRACTIONr_scangle_other7.7336.8442807
X-RAY DIFFRACTIONr_lrange_it7.87851.24332
X-RAY DIFFRACTIONr_lrange_other7.88451.1784323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.079-2.1330.3032100.2674019X-RAY DIFFRACTION99.389
2.133-2.1920.2752010.2413981X-RAY DIFFRACTION100
2.192-2.2550.2391840.2273877X-RAY DIFFRACTION99.9754
2.255-2.3250.2852030.2153730X-RAY DIFFRACTION99.9746
2.325-2.4010.2591730.2193639X-RAY DIFFRACTION99.9738
2.401-2.4850.2662030.2143478X-RAY DIFFRACTION99.9728
2.485-2.5790.2521640.2113393X-RAY DIFFRACTION100
2.579-2.6840.2561700.2253269X-RAY DIFFRACTION99.9709
2.684-2.8030.2921570.243161X-RAY DIFFRACTION100
2.803-2.940.2631530.253002X-RAY DIFFRACTION100
2.94-3.0990.2721590.2572840X-RAY DIFFRACTION100
3.099-3.2870.2921550.2432668X-RAY DIFFRACTION100
3.287-3.5140.2451390.2192552X-RAY DIFFRACTION100
3.514-3.7950.2171330.192363X-RAY DIFFRACTION100
3.795-4.1570.164920.142201X-RAY DIFFRACTION100
4.157-4.6470.1441090.131988X-RAY DIFFRACTION100
4.647-5.3640.173940.1281743X-RAY DIFFRACTION100
5.364-6.5660.18640.1571508X-RAY DIFFRACTION100
6.566-9.2720.153520.1451182X-RAY DIFFRACTION100

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