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- PDB-3ov4: Crystal Structure of Ketosteroid Isomerase P39GV40GS42G from Pseu... -

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Basic information

Entry
Database: PDB / ID: 3ov4
TitleCrystal Structure of Ketosteroid Isomerase P39GV40GS42G from Pseudomonas Testosteroni (tKSI) bound to Equilenin
ComponentsSteroid Delta-isomerase
KeywordsTRANSFERASE / Isomerase
Function / homology
Function and homology information


steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) 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 speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsGonzalez, A. / Tsai, Y. / Schwans, J. / Sunden, F. / Herschlag, D.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase P39GV40GS42G from Pseudomonas Testosteroni (tKSI)
Authors: Schwans, J. / Sunden, F. / Gonzalez, A. / Tsai, Y. / Herschlag, D.
History
DepositionSep 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_ref_seq_dif.details / _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: Steroid Delta-isomerase
B: Steroid Delta-isomerase
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,24820
Polymers53,2004
Non-polymers2,04816
Water9,044502
1
A: Steroid Delta-isomerase
B: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,80511
Polymers26,6002
Non-polymers1,2059
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-61 kcal/mol
Surface area12280 Å2
MethodPISA
2
C: Steroid Delta-isomerase
D: Steroid Delta-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4439
Polymers26,6002
Non-polymers8437
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-56 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.360, 64.360, 505.583
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-164-

HOH

21C-567-

HOH

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Components

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


Mass: 13299.934 Da / Num. of mol.: 4 / Mutation: P39G V40G S42G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (bacteria) / Strain: ATC 11996 / Gene: ksi / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EQU / EQUILENIN


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


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 10mg/ml protein, 1.8 M ammonium sulfate, 40mM potassium phosphate , 1 mM EDTA, 2mM DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9795
SYNCHROTRONSSRL BL9-120.9795
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDMar 24, 2010
ADSC QUANTUM 315r2CCDApr 7, 2010
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Si double crystalSINGLE WAVELENGTHx-ray1
2Si single crystalSINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.825→37.45 Å / Num. all: 56752 / Num. obs: 56752 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rsym value: 0.07 / Net I/σ(I): 25.8
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.83-1.872.30.3832834535790.38387.2
1.87-1.922.90.3322.41137438800.33296.6
1.92-1.985.10.2662.91963638370.26698
1.98-2.0410.40.2523.13959037970.252100
2.04-2.1112.70.2223.54741637230.222100
2.11-2.1813.30.19344784936060.193100
2.18-2.2613.60.1684.64687234540.168100
2.26-2.36140.15154729833790.151100
2.36-2.4614.40.1335.84667632400.133100
2.46-2.58150.1166.64662731140.116100
2.58-2.7215.60.0977.84587829480.097100
2.72-2.8916.30.0838.94589228100.083100
2.89-3.0917.20.06710.84597326800.067100
3.09-3.33180.05712.74491724910.057100
3.33-3.6518.90.05144369223130.05100
3.65-4.0819.70.04415.14208921410.044100
4.08-4.7120.30.03916.53865019020.039100
4.71-5.7720.50.03915.73395816540.039100
5.77-8.1620.70.03319.92804113540.033100
8.16-38.89117.80.02128.4151338500.02199

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å39.56 Å
Translation2 Å39.56 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8CHO

8cho


Resolution: 1.83→37.45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2065 / WRfactor Rwork: 0.1709 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8807 / SU B: 5.923 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1278 / SU Rfree: 0.1253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 2873 5.1 %RANDOM
Rwork0.1874 ---
all0.1894 56549 --
obs0.1894 56549 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 112.2 Å2 / Biso mean: 18.6023 Å2 / Biso min: 4.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.83→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 125 502 4310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224264
X-RAY DIFFRACTIONr_bond_other_d0.0020.022806
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9715840
X-RAY DIFFRACTIONr_angle_other_deg1.3973.0026738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28523.137204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62115663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6461542
X-RAY DIFFRACTIONr_chiral_restr0.1210.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024968
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02937
X-RAY DIFFRACTIONr_mcbond_it1.2241.52639
X-RAY DIFFRACTIONr_mcbond_other0.2551.51067
X-RAY DIFFRACTIONr_mcangle_it2.09824254
X-RAY DIFFRACTIONr_scbond_it2.99931625
X-RAY DIFFRACTIONr_scangle_it4.6014.51586
LS refinement shellResolution: 1.825→1.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 174 -
Rwork0.319 3392 -
all-3566 -
obs--86.76 %
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)
10.15770.0223-0.2340.0298-0.00890.3787-0.00690.00830.01750.01020.03080.00810.03370.0099-0.02390.02280.0065-0.00630.03430.00820.01430.91717.72628.094
20.2669-0.00020.01250.1493-0.10650.4726-0.0197-0.00310.03370.00660.03290.0102-0.0210.0323-0.01330.0032-0.00250.00050.03680.00320.01475.52932.28615.318
30.18580.0173-0.26070.0538-0.07290.4591-0.0092-0.05080.0004-0.01290.0076-0.00410.04390.0910.00160.01980.0062-0.00640.04110.00220.005416.70918.23918.664
40.2844-0.06580.10970.20320.19110.50550.014-0.0069-0.00860.00930.00790.00330.0095-0.0467-0.02190.0073-0.0051-0.00360.03150.00910.006227.21327.29435.295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION1A126 - 129
3X-RAY DIFFRACTION1A130 - 622
4X-RAY DIFFRACTION2B1 - 125
5X-RAY DIFFRACTION2B126 - 130
6X-RAY DIFFRACTION2B131 - 623
7X-RAY DIFFRACTION3C1 - 124
8X-RAY DIFFRACTION3C126 - 128
9X-RAY DIFFRACTION3C129 - 621
10X-RAY DIFFRACTION4D1 - 125
11X-RAY DIFFRACTION4D126 - 129
12X-RAY DIFFRACTION4D130 - 620

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