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

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Basic information

Entry
Database: PDB / ID: 8joj
TitleCrystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate
Components3-ketosteroid dehydrogenase
KeywordsOXIDOREDUCTASE / 3-ketosteroid delta1-dehydrogenase / Rhodococcus erythropolis SQ1 / 9 / 11-epoxy-17-hydroxypregn-4-ene-3 / 20-dione actate
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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-UU0 / 3-oxosteroid 1-dehydrogenase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.819 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 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate
Authors: Song, S.K. / Hu, Y.L. / Li, X. / Su, Z.D.
History
DepositionJun 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 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
A: 3-ketosteroid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8533
Polymers54,6511
Non-polymers1,2022
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.603, 119.603, 117.304
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-UU0 / 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate


Mass: 416.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32O6 / Feature type: SUBJECT OF INVESTIGATION
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: 72.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: UPH2O,3.5M Sodium formate 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: 2.819→103.58 Å / Num. obs: 22365 / % possible obs: 95.7 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 17.2
Reflection shellResolution: 2.82→2.97 Å / Rmerge(I) obs: 1.341 / Num. unique obs: 3357

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.819→77.764 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.171 / Average fsc free: 0.9001 / Average fsc work: 0.916 / Cross valid method: FREE R-VALUE / ESU R: 0.464 / ESU R Free: 0.294
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2345 1135 5.081 %
Rwork0.1887 21202 -
all0.191 --
obs-22337 95.703 %
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: 64.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.793 Å20.897 Å20 Å2
2--1.793 Å2-0 Å2
3----5.818 Å2
Refinement stepCycle: LAST / Resolution: 2.819→77.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 0 83 0 3925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134010
X-RAY DIFFRACTIONr_bond_other_d0.0370.0173595
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.6435469
X-RAY DIFFRACTIONr_angle_other_deg2.431.5758330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17722.304204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0715581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7451528
X-RAY DIFFRACTIONr_chiral_restr0.0660.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024664
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02833
X-RAY DIFFRACTIONr_nbd_refined0.2260.2861
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2330.23519
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21984
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.286
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.217
X-RAY DIFFRACTIONr_nbd_other0.2590.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.23
X-RAY DIFFRACTIONr_mcbond_it4.726.7752091
X-RAY DIFFRACTIONr_mcbond_other4.7116.7742090
X-RAY DIFFRACTIONr_mcangle_it6.68210.1632612
X-RAY DIFFRACTIONr_mcangle_other6.68310.1652613
X-RAY DIFFRACTIONr_scbond_it6.0467.2131919
X-RAY DIFFRACTIONr_scbond_other6.0447.2151920
X-RAY DIFFRACTIONr_scangle_it8.74210.6572854
X-RAY DIFFRACTIONr_scangle_other8.7410.6592855
X-RAY DIFFRACTIONr_lrange_it11.29680.6754356
X-RAY DIFFRACTIONr_lrange_other11.30280.6854357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.819-2.8920.348870.2831613X-RAY DIFFRACTION99.8238
2.892-2.9720.309900.2561561X-RAY DIFFRACTION100
2.972-3.0580.271870.2731572X-RAY DIFFRACTION100
3.058-3.1520.309570.271515X-RAY DIFFRACTION100
3.152-3.2550.316910.2351422X-RAY DIFFRACTION100
3.255-3.3690.27740.2231411X-RAY DIFFRACTION99.9327
3.369-3.4960.218560.219991X-RAY DIFFRACTION73.3193
3.496-3.6390.233610.1911339X-RAY DIFFRACTION100
3.639-3.80.264640.195863X-RAY DIFFRACTION71.7492
3.8-3.9850.208510.169982X-RAY DIFFRACTION80.3891
3.985-4.2010.182490.1571139X-RAY DIFFRACTION100
4.201-4.4550.189890.1511048X-RAY DIFFRACTION100
4.455-4.7620.167460.1281043X-RAY DIFFRACTION100
4.762-5.1430.205370.15954X-RAY DIFFRACTION100
5.143-5.6320.182470.16884X-RAY DIFFRACTION100
5.632-6.2950.328370.189810X-RAY DIFFRACTION100
6.295-7.2640.2360.182697X-RAY DIFFRACTION100
7.264-8.8850.23310.155615X-RAY DIFFRACTION100
8.885-12.520.176220.162472X-RAY DIFFRACTION100

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