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- PDB-1oho: CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE Y16F/D40N mutant COMPL... -

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Basic information

Entry
Database: PDB / ID: 1oho
TitleCRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE Y16F/D40N mutant COMPLEXED WITH EQUILENIN
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE / INHIBITOR / EQUILENIN
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
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, M.-S. / Byun, M. / Oh, B.-H.
CitationJournal: To be Published
Title: Crystal Structure of Ketosteroid Isomerase Y16F/D40N Mutant Complexed with Equilenin
Authors: Kim, M.-S. / Byun, M. / Oh, B.-H.
History
DepositionMay 29, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7982
Polymers14,5321
Non-polymers2661
Water75742
1
A: STEROID DELTA-ISOMERASE
hetero molecules

A: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5964
Polymers29,0632
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)36.122, 96.277, 74.262
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 STEROID DELTA-ISOMERASE / DELTA-5-3-KETOSTEROID / ISOMERASE


Mass: 14531.515 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07445, steroid Delta-isomerase
#2: Chemical ChemComp-EQU / EQUILENIN


Mass: 266.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: CONVERTS THE 3-OXO-DELTA(5)-STEROID TO THE 3-OXO-DELTA(4)-STEROID. ENGINEERED ...CATALYTIC ACTIVITY: CONVERTS THE 3-OXO-DELTA(5)-STEROID TO THE 3-OXO-DELTA(4)-STEROID. ENGINEERED MUTATION IN CHAIN A, ASP 40 TO ASN 40 ENGINEERED MUTATION IN CHAIN A, TYR 16 TO PHE 16

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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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growpH: 6.8 / Details: pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 1999 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→10 Å / Num. obs: 10600 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 29
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.2 / % possible all: 92.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.226 537 5 %RANDOM
Rwork0.196 ---
obs0.196 10149 96.8 %-
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 20 42 1018
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.641.5
X-RAY DIFFRACTIONc_mcangle_it2.6772
X-RAY DIFFRACTIONc_scbond_it2.6732
X-RAY DIFFRACTIONc_scangle_it4.0782.5
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.263 53
Rwork0.223 896

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