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- PDB-6ufs: Crystal structure of ketosteroid isomerase from Pseudomonas putid... -

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Basic information

Entry
Database: PDB / ID: 6ufs
TitleCrystal structure of ketosteroid isomerase from Pseudomonas putida (pKSI) bound to 5 alpha-dihydronandrolone
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE
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
5alpha-dihydronandrolone / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsWu, Y. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)GMR35-118044 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase.
Authors: Wu, Y. / Fried, S.D. / Boxer, S.G.
History
DepositionSep 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,3073
Polymers30,0302
Non-polymers2761
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-12 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.661, 73.481, 95.027
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: 15015.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-Q6J / 5alpha-dihydronandrolone / (5beta,9beta,10alpha,13alpha,14beta,17beta)-17-hydroxyestran-3-one


Mass: 276.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C18H28O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.1-1.4 M ammonium sulfate, 40 mM potassium phosphate, 3-6% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.35→36.74 Å / Num. obs: 55224 / % possible obs: 98.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.041 / Rrim(I) all: 0.103 / Net I/av σ(I): 7.2 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.35-1.374.280.7541.223670.8180.4070.86386.1
1.37-1.44.90.7061.426040.8360.3520.79495.1
1.4-1.426.20.6921.427480.8850.3010.75699.3
1.42-1.456.40.573227300.9340.9340.62499.9
1.45-1.496.40.4922.327960.930.2110.536100
1.49-1.526.40.4192.827030.8560.180.45799.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data scaling
PHASERphasing
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5D81

5d81


Resolution: 1.47→36.74 Å / Cross valid method: THROUGHOUT / σ(F): 1.34
RfactorNum. reflection% reflection
Rfree0.2205 2144 4.96 %
Rwork0.1882 --
obs0.1898 43215 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.25 Å2 / Biso mean: 23.427 Å2 / Biso min: 7.83 Å2
Refinement stepCycle: final / Resolution: 1.47→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 40 376 2398
Biso mean--21.17 35.1 -
Num. residues----255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.50.27471310.238727212852100
1.5-1.540.24341280.22927222850100
1.54-1.580.23831400.23192653279399
1.58-1.630.2311440.20652707285199
1.63-1.680.23331520.200426772829100
1.68-1.740.23161420.202227042846100
1.74-1.810.24181350.201427082843100
1.81-1.90.21491330.20292722285599
1.9-1.990.2391300.196127542884100
2-2.120.24531330.196527352868100
2.12-2.280.20211500.186627272877100
2.28-2.510.22751450.194627502895100
2.51-2.880.22421610.190327522913100
2.88-3.620.21121610.168527912952100
3.63-36.740.20591590.172929483107100

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