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- PDB-3owu: Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/F8... -

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Basic information

Entry
Database: PDB / ID: 3owu
TitleCrystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/F86C-CN from P. putida with Bound Equilenin
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / steroids / cyanylation
Function / homology
Function and homology information


steroid Delta-isomerase / steroid Delta-isomerase activity / steroid metabolic process
Similarity search - Function
Ketosteroid isomerase / SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSigala, P.A. / Fenn, T.D. / Herschlag, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase.
Authors: Fafarman, A.T. / Sigala, P.A. / Schwans, J.P. / Fenn, T.D. / Herschlag, D. / Boxer, S.G.
History
DepositionSep 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Mar 7, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9878
Polymers57,9214
Non-polymers1,0654
Water3,927218
1
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4934
Polymers28,9612
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-10 kcal/mol
Surface area12590 Å2
MethodPISA
2
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4934
Polymers28,9612
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-9 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.231, 130.329, 45.131
Angle α, β, γ (deg.)90.000, 112.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Steroid Delta-isomerase / Delta(5)-3-ketosteroid isomerase


Mass: 14480.298 Da / Num. of mol.: 4 / Mutation: D40N, C69S, C81S, F86(XCN), C97S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical
ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.1 M ammonium sulfate, 5% isopropanol, 40 mM potassium phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2007
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→36.14 Å / Num. all: 52609 / Num. obs: 32425 / % possible obs: 62 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.26 Å2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 2

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PZV

2pzv


Resolution: 1.7→36.14 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.682 / SU ML: 1.5 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1497 5.03 %random
Rwork0.2157 ---
obs0.2185 29769 56.66 %-
all-52609 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.163 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso max: 134.24 Å2 / Biso mean: 45.2354 Å2 / Biso min: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1-3.9362 Å2-0 Å28.9595 Å2
2---16.0116 Å20 Å2
3----5.9968 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3984 0 80 218 4282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054160
X-RAY DIFFRACTIONf_angle_d1.0595664
X-RAY DIFFRACTIONf_chiral_restr0.06596
X-RAY DIFFRACTIONf_plane_restr0.003752
X-RAY DIFFRACTIONf_dihedral_angle_d16.991528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.75830.372150.41683882
1.7583-1.82110.5359120.32063543668
1.8211-1.8940.3941380.292781485218
1.894-1.98020.425780.30021375145331
1.9802-2.08460.27971100.27442108221847
2.0846-2.21520.32291300.25622781291161
2.2152-2.38620.36481800.25233420360075
2.3862-2.62630.30062130.26494022423589
2.6263-3.00610.32142450.24824347459296
3.0061-3.78680.24732660.19774400466698
3.7868-36.140.20432200.16514568478899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.29050.385-0.08381.308-0.83681.10470.01-0.02280.05430.0132-0.1709-0.2921-0.18170.13240.14480.226-0.027-0.00530.2171-0.01370.21819.3404-5.28862.8183
20.1354-0.55940.14111.72730.54040.6168-0.017-0.0314-0.1232-0.11710.01490.3114-0.10820.01740.00360.2335-0.01810.00720.205-0.00450.2753-7.6614-18.066-6.3853
31.2641-0.0152-0.10340.2804-0.15931.28730.037-0.0595-0.1368-0.0091-0.1052-0.22040.18860.06160.05760.1979-0.02310.02220.1873-0.02570.218416.925613.0668-16.503
41.23860.5857-0.37741.053-0.06410.7364-0.05220.0130.2086-0.0863-0.05310.03730.1539-0.02430.08010.1509-0.0243-0.010.20260.00560.1809-1.79525.466-21.6812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 130
2X-RAY DIFFRACTION2chain BB2 - 130
3X-RAY DIFFRACTION3chain CC2 - 130
4X-RAY DIFFRACTION4chain DD2 - 130

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