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- PDB-5kp4: Crystal Structure of Ketosteroid Isomerase from Pseudomonas putid... -

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Basic information

Entry
Database: PDB / ID: 5kp4
TitleCrystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI) bound to 19-nortestosterone
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
Chem-6VW / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.706 Å
AuthorsWu, Y. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM27738 and GM118044 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase.
Authors: Wu, Y. / Boxer, S.G.
History
DepositionJul 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)30,3053
Polymers30,0302
Non-polymers2741
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-12 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.851, 72.587, 94.820
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-6VW / (8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-methyl-17-oxidanyl-2,6,7,8,9,10,11,12,14,15,16,17-dodecahydro-1~{H}-cyclop enta[a]phenanthren-3-one / 19-nortestosterone


Mass: 274.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C18H26O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsfor the reference, 19-Nortestosterone binds to WT-KSI protein with Kd ~8uM as was previously ...for the reference, 19-Nortestosterone binds to WT-KSI protein with Kd ~8uM as was previously reported by Kim et al. Biochemistry 38 (1999) 13810-19

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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: 1.94 Å3/Da / Density % sol: 36.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.1-1.4M ammonium sulfate, 40mM potassium phosphate, 3-6% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.706→36.294 Å / Num. obs: 26203 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.706→36.294 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34
RfactorNum. reflection% reflection
Rfree0.239 1306 5 %
Rwork0.2032 --
obs0.205 26144 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.56 Å2 / Biso mean: 30.7517 Å2 / Biso min: 13.23 Å2
Refinement stepCycle: final / Resolution: 1.706→36.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 20 138 2121
Biso mean--36.39 35.11 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062050
X-RAY DIFFRACTIONf_angle_d0.8512792
X-RAY DIFFRACTIONf_chiral_restr0.052300
X-RAY DIFFRACTIONf_plane_restr0.005374
X-RAY DIFFRACTIONf_dihedral_angle_d16.8911228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.706-1.77430.28831420.252927032845
1.7743-1.85510.24211410.234226892830
1.8551-1.95290.27371440.215727142858
1.9529-2.07520.27441430.221327342877
2.0752-2.23540.21981430.208927292872
2.2354-2.46040.22931440.209227492893
2.4604-2.81630.24251470.210127922939
2.8163-3.54770.20591470.204727882935
3.5477-36.30170.24781550.182829403095

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