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- PDB-4k1u: Crystal structure of delta5-3-ketosteroid isomerase containing Y1... -

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Basic information

Entry
Database: PDB / ID: 4k1u
TitleCrystal structure of delta5-3-ketosteroid isomerase containing Y16F and Y32F mutations
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / Cystatin-like fold / allylic isomerization / delta5-3ketosteroids / cytosol
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 / Resolution: 2 Å
AuthorsCha, H.J. / Jang, D.S. / Kim, Y.G. / Hong, B.H. / Woo, J.S. / Choi, K.Y.
CitationJournal: Mol.Cells / Year: 2013
Title: Rescue of deleterious mutations by the compensatory Y30F mutation in ketosteroid isomerase
Authors: Cha, H.J. / Jang, D.S. / Kim, Y.G. / Hong, B.H. / Woo, J.S. / Kim, K.T. / Choi, K.Y.
History
DepositionApr 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)29,0332
Polymers29,0332
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-11 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.284, 73.094, 95.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14516.501 Da / Num. of mol.: 2 / Mutation: Y16F Y32F
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: SODIUM ACETATE, AMMONIUM ACETATE, pH 4.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 15, 2007
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 28818 / Num. obs: 16266 / % possible obs: 56.4 % / Observed criterion σ(I): 0
Reflection shellResolution: 2→2 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 1361 / Rsym value: 0.184 / % possible all: 81

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 786 RANDOM
Rwork0.225 --
all-16789 -
obs-16120 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1890 0 0 94 1984
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.464
X-RAY DIFFRACTIONc_angle_deg2.335

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