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- PDB-4qdf: Crystal structure of apo KshA5 and KshA1 in complex with 1,4-30Q-... -

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Basic information

Entry
Database: PDB / ID: 4qdf
TitleCrystal structure of apo KshA5 and KshA1 in complex with 1,4-30Q-CoA from R. rhodochrous
Components(3-ketosteroid 9alpha-hydroxylase ...) x 2
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 / steroid metabolic process / cholesterol catabolic process / lipid 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 / PHOSPHATE ION / 3-ketosteroid-9-alpha-monooxygenase, oxygenase component / 3-ketosteroid-9-alpha-monooxygenase, oxygenase component
Similarity search - Component
Biological speciesRhodococcus rhodochrous (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.43 Å
AuthorsPenfield, J. / Worrall, L.J. / Strynadka, N.C. / Eltis, L.D.
Citation
Journal: 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_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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
B: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,67410
Polymers89,3712
Non-polymers1,3028
Water3,621201
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)134,44515
Polymers132,8913
Non-polymers1,55412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area8490 Å2
ΔGint-129 kcal/mol
Surface area46860 Å2
MethodPISA
2
B: 3-ketosteroid 9alpha-hydroxylase oxygenase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)137,57615
Polymers135,2233
Non-polymers2,35312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_545-y,z-1/2,-x+1/21
crystal symmetry operation31_555-z+1/2,-x,y+1/21
Buried area10740 Å2
ΔGint-173 kcal/mol
Surface area48060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)273.680, 273.680, 273.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

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Components

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3-ketosteroid 9alpha-hydroxylase ... , 2 types, 2 molecules AB

#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: Protein 3-ketosteroid 9alpha-hydroxylase oxygenase


Mass: 45074.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus rhodochrous (bacteria) / Gene: kshA1 / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158 / References: UniProt: F1CMX0

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Non-polymers , 7 types, 209 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: 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
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 4.78 Å3/Da / Density % sol: 74.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 500 mM NaH2PO4, 125 mM K2HPO4, 4% PEG- 1000, 20 mM Tris, 100 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: 0.92 Å
DetectorType: Rayonix MX300HE CCD X-ray detector / 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: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.43→68.41 Å / Num. all: 64010 / Num. obs: 64010 / % possible obs: 100 % / Redundancy: 14.7 % / Rmerge(I) obs: 0.176 / Net I/σ(I): 12.6 / Scaling rejects: 278
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
2.43-2.4914.32645134518100
11.11-68.4113.533.6971471799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHASERphasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
MxDCdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→68.42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.1949 / WRfactor Rwork: 0.1668 / FOM work R set: 0.8515 / SU B: 5.999 / SU ML: 0.13 / SU R Cruickshank DPI: 0.188 / SU Rfree: 0.1678 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 3222 5.1 %RANDOM
Rwork0.185 ---
obs0.1865 63637 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 138.58 Å2 / Biso mean: 49.586 Å2 / Biso min: 22.69 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.43→68.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5828 0 60 201 6089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196057
X-RAY DIFFRACTIONr_bond_other_d0.0020.025459
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.938225
X-RAY DIFFRACTIONr_angle_other_deg0.7433.00212554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08823.82322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22215949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0811543
X-RAY DIFFRACTIONr_chiral_restr0.0710.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021501
X-RAY DIFFRACTIONr_mcbond_it2.9464.7932865
X-RAY DIFFRACTIONr_mcbond_other2.9424.7912864
X-RAY DIFFRACTIONr_mcangle_it4.787.1733576
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 235 -
Rwork0.302 4428 -
all-4663 -
obs--100 %

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