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- PDB-4qdd: Crystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) ... -

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Basic information

Entry
Database: PDB / ID: 4qdd
TitleCrystal structure of 3-ketosteroid-9-alpha-hydroxylase 5 (KshA5) from R. rhodochrous in complex with 1,4-30Q-CoA
Components3-ketosteroid 9alpha-hydroxylase oxygenase
Keywordsoxidoreductase/oxidoreductase inhibitor / Mixed Function Oxygenases / oxidoreductase-oxidoreductase inhibitor complex
Function / homology
Function and homology information


3-ketosteroid 9alpha-monooxygenase / 3-ketosteroid 9-alpha-monooxygenase activity / cholesterol catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
3-ketosteroid-9-alpha-monooxygenase, oxygenase component-like, C-terminal domain / 3-Ketosteroid 9alpha-hydroxylase C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. ...3-ketosteroid-9-alpha-monooxygenase, oxygenase component-like, C-terminal domain / 3-Ketosteroid 9alpha-hydroxylase C-terminal domain / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-30Q / : / FE2/S2 (INORGANIC) CLUSTER / 3-ketosteroid-9-alpha-monooxygenase, oxygenase component
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsPenfield, J. / Worrall, L.J. / Strynadka, N.C. / Eltis, L.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Substrate specificities and conformational flexibility of 3-ketosteroid 9 alpha-hydroxylases.
Authors: Penfield, J.S. / Worrall, L.J. / Strynadka, N.C. / Eltis, L.D.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9864
Polymers44,2971
Non-polymers6893
Water41423
1
A: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules

A: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules

A: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,95912
Polymers132,8913
Non-polymers2,0689
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area12180 Å2
ΔGint-150 kcal/mol
Surface area48450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.170, 163.170, 47.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein 3-ketosteroid 9alpha-hydroxylase oxygenase


Mass: 44297.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: kshA5 / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158 / References: UniProt: F1CMY8
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-30Q / S-[2-(propanoylamino)ethyl] (2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-dimethyl-3-oxo-6,7,8,9,10,11,12,13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthren-17-yl]propanethioate (non-preferred name)


Mass: 457.668 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H39NO3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 4.09 Å3/Da / Density % sol: 69.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.5 M NaH2PO4, 0.125 M K2HPO4, 4% PEG-1000, 20 mM Tris, 0.1 mM phosphate-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 24, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.662
11K, H, -L20.338
ReflectionResolution: 2.6→141.309 Å / Num. all: 22485 / Num. obs: 22485 / % possible obs: 100 % / Redundancy: 6.7 % / Rsym value: 0.244 / Net I/σ(I): 7.1
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.746.20.62029932481.278100
2.74-2.916.40.81967230681.025100
2.91-3.116.61.11908028890.742100
3.11-3.366.81.61857627120.475100
3.36-3.6872.71736824870.292100
3.68-4.1173.71571422470.21100
4.11-4.756.95.41396220090.142100
4.75-5.816.96.11190917200.123100
5.81-8.226.87.1909913340.1100
8.22-53.416.514.849817710.04399.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
MxDCdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→53.41 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.871 / WRfactor Rfree: 0.2398 / WRfactor Rwork: 0.2131 / FOM work R set: 0.7893 / SU R Cruickshank DPI: 0.0719 / SU Rfree: 0.0539 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1117 5 %RANDOM
Rwork0.2249 ---
obs0.2265 22477 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.16 Å2 / Biso mean: 50.678 Å2 / Biso min: 21.01 Å2
Baniso -1Baniso -2Baniso -3
1-18.07 Å20 Å20 Å2
2--18.07 Å20 Å2
3----36.14 Å2
Refinement stepCycle: LAST / Resolution: 2.6→53.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2959 0 37 23 3019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023082
X-RAY DIFFRACTIONr_bond_other_d00.022786
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.9374193
X-RAY DIFFRACTIONr_angle_other_deg3.6433.0046412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75624.136162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09515482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9961520
X-RAY DIFFRACTIONr_chiral_restr0.0580.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213521
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02752
X-RAY DIFFRACTIONr_mcbond_it2.6295.1561462
X-RAY DIFFRACTIONr_mcbond_other2.6175.1531461
X-RAY DIFFRACTIONr_mcangle_it3.997.7231824
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 71 -
Rwork0.265 1566 -
all-1637 -
obs--99.94 %

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