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- PDB-3vsy: High-resolution crystal structure of wild-type KSI in the apo for... -

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Basic information

Entry
Database: PDB / ID: 3vsy
TitleHigh-resolution crystal structure of wild-type KSI in the apo form at neutral pH
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / Alpha-beta roll / Steroid / OXYANION-HOLE / Intracellular
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 / molecular replacement / Resolution: 1.5 Å
AuthorsCaaveiro, J.M.M. / Kobe, A. / Tsumoto, K.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Incorporation of rapid thermodynamic data in fragment-based drug discovery.
Authors: Kobe, A. / Caaveiro, J.M.M. / Tashiro, S. / Kajihara, D. / Kikkawa, M. / Mitani, T. / Tsumoto, K.
History
DepositionMay 16, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,2014
Polymers29,0092
Non-polymers1922
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-31 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.563, 73.353, 95.549
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14504.382 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 3-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.15 Å3/Da / Density % sol: 42.74 % / Mosaicity: 0.398 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: AMMONIUM SULPHATE 1.4M, 2-PROPANOL 5-7%, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2011 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Number: 276228 / Rmerge(I) obs: 0.058 / Χ2: 1.02 / D res high: 1.5 Å / D res low: 58.18 Å / Num. obs: 40264 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.235099.210.0350.996.8
2.563.2310010.0480.9887.2
2.242.5610010.0640.9737.3
2.042.2410010.0810.9847.3
1.892.0410010.1140.9927.3
1.781.8910010.1671.0197.2
1.691.7810010.2391.0617.2
1.621.6910010.3431.0757.2
1.551.6297.310.3931.0726
1.51.558410.491.0314.8
ReflectionResolution: 1.5→58.18 Å / Num. all: 41000 / Num. obs: 40264 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 17
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / Num. unique all: 3395 / % possible all: 84

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.08 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.21 Å
Translation2.5 Å29.21 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CPO

3cpo


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2106 / WRfactor Rwork: 0.1601 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8701 / SU B: 2.841 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0809 / SU Rfree: 0.0747 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 1605 4 %RANDOM
Rwork0.1503 ---
all0.1523 41000 --
obs0.1523 40065 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 88.13 Å2 / Biso mean: 26.8173 Å2 / Biso min: 12.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2---0.12 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 10 250 2180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192051
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.952800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6955271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09223.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79515337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5941520
X-RAY DIFFRACTIONr_chiral_restr0.1170.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211616
X-RAY DIFFRACTIONr_rigid_bond_restr4.60732051
X-RAY DIFFRACTIONr_sphericity_free30.884568
X-RAY DIFFRACTIONr_sphericity_bonded15.25852183
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 89 -
Rwork0.202 2232 -
all-2321 -
obs--81.18 %

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