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Basic information

Entry
Database: PDB / ID: 1opy
TitleKSI
ComponentsDELTA5-3-KETOSTEROID IOSMERASE
KeywordsISOMERASE / KSI / HIGH RESOLUTION / PSEUDOMONAS PUTIDA BIOTYPE B / LOW-BARRIER HYDROGEN BOND
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 / Resolution: 1.9 Å
AuthorsKim, S.-W. / Cha, S.-S. / Cho, H.-S. / Kim, J.-S. / Ha, N.-C. / Cho, M.-J. / Choi, K.-Y. / Oh, B.-H.
CitationJournal: Biochemistry / Year: 1997
Title: High-resolution crystal structures of delta5-3-ketosteroid isomerase with and without a reaction intermediate analogue.
Authors: Kim, S.W. / Cha, S.S. / Cho, H.S. / Kim, J.S. / Ha, N.C. / Cho, M.J. / Joo, S. / Kim, K.K. / Choi, K.Y. / Oh, B.H.
History
DepositionMay 23, 1997Processing site: BNL
Revision 1.0Apr 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DELTA5-3-KETOSTEROID IOSMERASE


Theoretical massNumber of molelcules
Total (without water)14,5491
Polymers14,5491
Non-polymers00
Water86548
1
A: DELTA5-3-KETOSTEROID IOSMERASE

A: DELTA5-3-KETOSTEROID IOSMERASE


Theoretical massNumber of molelcules
Total (without water)29,0972
Polymers29,0972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)36.400, 96.120, 74.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DELTA5-3-KETOSTEROID IOSMERASE / KSI / 3-KETOSTEROID ISOMERASE


Mass: 14548.501 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: BIOTYPE B / Plasmid: DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.4 Msodium acetate1reservoir
20.1 Mammonium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Dec 11, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 6679 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.06
Reflection
*PLUS
Highest resolution: 1.9 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 1.9→10 Å / σ(F): 1
RfactorNum. reflection
Rfree0.273 -
Rwork0.199 -
obs0.199 200000
Displacement parametersBiso mean: 26 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 0 28 985
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.595
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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