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- PDB-5d81: Crystal Structure of Ketosteroid Isomerase from Pseudomonas putid... -

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Basic information

Entry
Database: PDB / ID: 5d81
TitleCrystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI); D40N, Y57(Cl-Y)
ComponentsDelta(5)-3-ketosteroid 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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.39 Å
AuthorsWu, Y. / Fried, S.D. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochemistry / Year: 2015
Title: Dissecting Proton Delocalization in an Enzyme's Hydrogen Bond Network with Unnatural Amino Acids.
Authors: Wu, Y. / Fried, S.D. / Boxer, S.G.
History
DepositionAug 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Data collection
Revision 1.2Dec 25, 2019Group: 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 1.3Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Delta(5)-3-ketosteroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2413
Polymers15,0491
Non-polymers1922
Water1,964109
1
A: Delta(5)-3-ketosteroid isomerase
hetero molecules

A: Delta(5)-3-ketosteroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4816
Polymers30,0972
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2630 Å2
ΔGint-49 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.650, 94.831, 72.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

21A-351-

HOH

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Components

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


Mass: 15048.559 Da / Num. of mol.: 1 / Mutation: D40N,Y57(Cl-Y)
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-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.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.39 %
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
PH range: 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.39→47.415 Å / Num. all: 25007 / Num. obs: 25007 / % possible obs: 98.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 15.48 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.041 / Rsym value: 0.036 / Net I/av σ(I): 8.931 / Net I/σ(I): 18.4 / Num. measured all: 105804
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.39-1.474.30.2063.71567936300.1080.2065.799.5
1.47-1.553.90.135.81347734140.0720.137.898.6
1.55-1.664.40.0898.21421032240.0460.08911.299.5
1.66-1.794.10.0699.71245330070.0360.06914.399.1
1.79-1.974.10.057111139327640.030.05719.298.6
1.97-2.24.40.04413.41114225050.0230.04425.798.6
2.2-2.544.10.03318.2925022420.0180.03328.998.6
2.54-3.114.50.03415.2855518820.0170.03434.598.6
3.11-4.44.10.03217.5607314780.0160.03237.397.8
4.4-47.4154.10.02520.635728610.0130.02537.897.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
RefinementResolution: 1.39→47.415 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 1270 5.08 %
Rwork0.1876 23716 -
obs0.1893 24986 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.39 Å2 / Biso mean: 25.0638 Å2 / Biso min: 8.85 Å2
Refinement stepCycle: final / Resolution: 1.39→47.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 10 109 1100
Biso mean--51.72 32.95 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071050
X-RAY DIFFRACTIONf_angle_d1.0571436
X-RAY DIFFRACTIONf_chiral_restr0.045151
X-RAY DIFFRACTIONf_plane_restr0.005192
X-RAY DIFFRACTIONf_dihedral_angle_d15.07392
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 (%)
1.39-1.44560.25591480.21852618276699
1.4456-1.51140.22741420.21562584272699
1.5114-1.59110.21361530.19922599275298
1.5911-1.69080.25661170.2022671278899
1.6908-1.82140.22441490.19412575272498
1.8214-2.00470.22151240.1952640276498
2.0047-2.29470.23091480.19052622277098
2.2947-2.89110.25191480.19282659280799
2.8911-47.44280.19551410.17232748288997

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