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- PDB-3ox9: Crystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/F8... -

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Basic information

Entry
Database: PDB / ID: 3ox9
TitleCrystal Structure of Ketosteroid Isomerase D40N/C69S/C81S/C97S/F86C-CN from P. putida
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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 21, 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_ncs_dom_lim / struct_ref_seq_dif
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,9214
Polymers57,9214
Non-polymers00
Water1,38777
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)28,9612
Polymers28,9612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-12 kcal/mol
Surface area12380 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)28,9612
Polymers28,9612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-12 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.128, 129.842, 45.193
Angle α, β, γ (deg.)90.000, 114.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 2 - 127 / Label seq-ID: 2 - 127

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 2:127 )AA
2chain B and (resseq 2:127 )BB
3chain C and (resseq 2:127 )CC
4chain D and (resseq 2:127 )DD

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
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: Oct 23, 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: 2→41.13 Å / Num. all: 31289 / Num. obs: 25499 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.23 Å2
Reflection shellResolution: 2→2.08 Å / % possible all: 21

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
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→41.13 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6679 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3408 1199 5.02 %random
Rwork0.2645 ---
obs0.2683 23898 76.44 %-
all-31289 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.054 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso max: 166.29 Å2 / Biso mean: 43.9055 Å2 / Biso min: 3.67 Å2
Baniso -1Baniso -2Baniso -3
1--4.3702 Å2-0 Å25.349 Å2
2---0.6813 Å2-0 Å2
3---4.2048 Å2
Refinement stepCycle: LAST / Resolution: 2→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3984 0 0 77 4061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094068
X-RAY DIFFRACTIONf_angle_d1.0845520
X-RAY DIFFRACTIONf_chiral_restr0.073588
X-RAY DIFFRACTIONf_plane_restr0.004748
X-RAY DIFFRACTIONf_dihedral_angle_d18.3111508
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A969X-RAY DIFFRACTIONPOSITIONAL0.064
12B969X-RAY DIFFRACTIONPOSITIONAL0.064
13C969X-RAY DIFFRACTIONPOSITIONAL0.065
14D969X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07880.3266330.34268471721
2.0788-2.17340.4317670.31391371143842
2.1734-2.2880.40781290.31122154228366
2.288-2.43130.35471310.30592705283682
2.4313-2.6190.42351490.30462965311490
2.619-2.88250.33871750.29293070324594
2.8825-3.29940.33251670.27873168333596
3.2994-4.15630.32691710.24393255342698
4.1563-41.130.2941770.219233273504100
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)
10.77270.0234-0.21430.29020.31020.1980.02230.1397-0.1930.0263-0.15860.09960.0384-0.137500.0250.0020.00860.111-0.03590.11254.85365.342516.2718
20.85950.59930.76931.68360.21120.53880.22270.10250.0218-0.0199-0.1916-0.2962-0.0025-0.16970.00640.01550.00910.0093-0.01570.01320.057422.997518.503321.9566
30.7933-0.22340.4150.4312-0.38760.37010.0248-0.0219-0.1142-0.1569-0.10820.11110.06520.0923-0.00590.1437-0.01530.00710.054-0.02670.0683-5.007439.636734.3122
40.38770.34170.2421.1174-0.60010.7630.2337-0.49890.42760.1597-0.9718-0.2892-0.09010.5765-0.13630.1012-0.161-0.010.17520.2081-0.020612.006552.307543.6207
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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