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- PDB-4k1v: Crystal structure of delta5-3-ketosteroid isomerase containing Y1... -

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Basic information

Entry
Database: PDB / ID: 4k1v
TitleCrystal structure of delta5-3-ketosteroid isomerase containing Y16F and Y57F 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: 1.8 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 1.2Nov 8, 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 / 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


Theoretical massNumber of molelcules
Total (without water)14,5171
Polymers14,5171
Non-polymers00
Water1,22568
1
A: Steroid Delta-isomerase

A: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)29,0332
Polymers29,0332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2130 Å2
ΔGint-11 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.347, 94.723, 73.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

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Components

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


Mass: 14516.501 Da / Num. of mol.: 1 / Mutation: Y16F, Y57F
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.: 68 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
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: 1.8→50 Å / Num. all: 19423 / Num. obs: 10879 / % possible obs: 56 % / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.8 Å / Redundancy: 3 % / Mean I/σ(I) obs: 12.4 / Num. unique all: 956 / Rsym value: 0.128 / % possible all: 82

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OPY

1opy


Resolution: 1.8→20 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.207 569 random
Rwork0.2 --
all-11874 -
obs-10875 -
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 0 68 1026
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.22
X-RAY DIFFRACTIONc_angle_deg1.81

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