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- PDB-1k41: Crystal structure of KSI Y57S mutant -

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Basic information

Entry
Database: PDB / ID: 1k41
TitleCrystal structure of KSI Y57S mutant
ComponentsKetosteroid Isomerase
KeywordsISOMERASE / KSI Y57S Helix
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCha, S.S. / Oh, B.H. / Nam, G.H. / Jang, D.S. / Lee, T.H. / Choi, K.Y.
CitationJournal: Biochemistry / Year: 2001
Title: Maintenance of alpha-helical structures by phenyl rings in the active-site tyrosine triad contributes to catalysis and stability of ketosteroid isomerase from Pseudomonas putida biotype B
Authors: Nam, G.H. / Jang, D.S. / Cha, S.S. / Lee, T.H. / Kim, D.H. / Hong, B.H. / Yun, Y.S. / Oh, B.H. / Choi, K.Y.
History
DepositionOct 5, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketosteroid Isomerase
B: Ketosteroid Isomerase


Theoretical massNumber of molelcules
Total (without water)28,9452
Polymers28,9452
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-10 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.889, 73.135, 51.156
Angle α, β, γ (deg.)90.00, 89.85, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe active form of KSI is dimer

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Components

#1: Protein Ketosteroid Isomerase / Steroid delta-isomerase


Mass: 14472.403 Da / Num. of mol.: 2 / Mutation: Y57S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 4.6
Details: Sodium Acetate, Ammonium acetate, pH 4.6, EVAPORATION, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2 Mammonium acetate1reservoir
20.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 18, 1997 / Details: monochromator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 20000 / Num. obs: 15486 / % possible obs: 94.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.4 Å / % possible all: 82
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.315 774 4.998 %
Rwork0.235 --
all0.235 20000 -
obs0.235 15486 -
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 0 41 1896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.083
X-RAY DIFFRACTIONx_angle_deg3.172
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.235 / Rfactor Rfree: 0.319 / Rfactor Rwork: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS

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