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- PDB-3owy: Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M1... -

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Basic information

Entry
Database: PDB / ID: 3owy
TitleCrystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/M105C-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: 2.3 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 1.5Nov 6, 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
E: Steroid Delta-isomerase
F: Steroid Delta-isomerase
G: Steroid Delta-isomerase
H: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,56814
Polymers115,9708
Non-polymers1,5986
Water2,378132
1
A: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5254
Polymers28,9932
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-9 kcal/mol
Surface area12690 Å2
MethodPISA
2
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5254
Polymers28,9932
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-9 kcal/mol
Surface area12630 Å2
MethodPISA
3
E: Steroid Delta-isomerase
H: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5254
Polymers28,9932
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-8 kcal/mol
Surface area12410 Å2
MethodPISA
4
F: Steroid Delta-isomerase
G: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)28,9932
Polymers28,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-12 kcal/mol
Surface area12760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.326, 129.426, 83.988
Angle α, β, γ (deg.)90.000, 96.480, 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: 14496.276 Da / Num. of mol.: 8 / Mutation: D40N, C69S, C81S, C97S, M105(XCN)
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.: 6 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
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: Feb 19, 2008
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: 2.3→36.36 Å / Num. all: 42539 / Num. obs: 39308 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.62 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 52

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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: 2.3→36.36 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6115 / SU ML: 1.96 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3461 1555 5.09 %random
Rwork0.2797 ---
obs0.2831 30580 71.96 %-
all-42539 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.365 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso max: 150.54 Å2 / Biso mean: 62.7312 Å2 / Biso min: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1--25.6997 Å2-0 Å21.1798 Å2
2---21.0644 Å2-0 Å2
3---13.0726 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7992 0 120 132 8244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048306
X-RAY DIFFRACTIONf_angle_d0.84711304
X-RAY DIFFRACTIONf_chiral_restr0.0441188
X-RAY DIFFRACTIONf_plane_restr0.0031510
X-RAY DIFFRACTIONf_dihedral_angle_d15.0273030
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 (%)
2.3-2.37840.4711990.34591920201952
2.3784-2.46340.45861120.35392006211856
2.4634-2.5620.44531280.3252226235461
2.562-2.67850.40141240.31932485260967
2.6785-2.81970.36241170.32242726284374
2.8197-2.99630.34681530.29432844299778
2.9963-3.22750.32141470.28072814296176
3.2275-3.5520.33531460.25792752289876
3.552-4.06540.32811790.25712939311881
4.0654-5.11980.28471650.22313056322183
5.1198-36.360.33041850.26593257344288
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)
10.0550.0241-0.02090.0580.00840.00050.0579-0.00890.0690.0608-0.1413-0.05460.0082-0.0801-0.01670.0551-0.07590.0155-0.10920.18150.46919.67377.57169.3923
2-0.02480.07120.00460.12780.05150.0720.0067-0.016-0.04430.0279-0.0422-0.02530.04720.00180.00860.0917-0.04090.0676-0.04270.01920.4186-0.8409-26.34249.4151
30.4757-0.4025-0.01840.6970.06130.13910.07670.1466-0.0288-0.1887-0.2644-0.1319-0.0245-0.11770.00780.06440.0535-0.03210.04510.0210.4498-3.1698-13.9793-9.9628
4-0.0756-0.09860.05710.0487-0.06480.068-0.02880.05670.2520.0192-0.1042-0.086-0.07170.07790.04980.12550.0241-0.0120.06450.05350.222721.65720.2523-9.9397
50.03790.00920.00260.2026-0.00930.00310.1253-0.05320.00990.085-0.0659-0.06930.0452-0.0958-0.04471.18590.0249-0.27720.269-0.12510.14191.67337.3-32.3234
60.15110.01230.02410.0530.0306-0.0851-0.1501-0.378-0.03410.10120.0164-0.051-0.1531-0.02240.03971.10950.1518-0.45880.549-0.1329-0.1731-18.8386-26.4914-32.2219
70.0842-0.0156-0.04070.090.0436-0.04380.026-0.1542-0.07280.03770.0685-0.0217-0.20070.1815-0.03240.9617-0.2222-0.09660.3612-0.0052-0.346-21.2578-14.4029-51.6752
80.1984-0.0342-0.0086-0.07730.03010.22940.1987-0.1615-0.0054-0.2781-0.09610.2526-0.10150.066-0.06251.0727-0.0077-0.30590.29580.11920.55655.7083-44.7643-31.7763
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
5X-RAY DIFFRACTION5chain EE2 - 130
6X-RAY DIFFRACTION6chain FF2 - 130
7X-RAY DIFFRACTION7chain GG2 - 130
8X-RAY DIFFRACTION8chain HH2 - 130

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