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- PDB-1ohp: CRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT D38N FROM P... -

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Basic information

Entry
Database: PDB / ID: 1ohp
TitleCRYSTAL STRUCTURE OF 5-3-KETOSTEROID ISOMERASE MUTANT D38N FROM PSEUDOMONAS TESTOSTERONI COMPLEXED WITH 5ALPHA-ESTRAN-3,17-DIONE
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE / INHIBITOR
Function / homology
Function and homology information


steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process
Similarity search - Function
Steroid delta5-4-isomerase / Ketosteroid isomerase / Nuclear transport factor 2 (NTF2) domain / 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
5-ALPHA-ESTRAN-3,17-DIONE / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS TESTOSTERONI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.53 Å
AuthorsByun, M. / Kim, M.-S. / Oh, B.-H.
CitationJournal: To be Published
Title: Crystal Structure of 5-3-Ketosteroid Isomerase Mutant D38N from Pseudomonas Testosteroni Complexed with 5Alpha-Estran-3,17-Dione
Authors: Byun, M. / Kim, M.-S. / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

Deposited unit
A: STEROID DELTA-ISOMERASE
B: STEROID DELTA-ISOMERASE
C: STEROID DELTA-ISOMERASE
D: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7908
Polymers53,6934
Non-polymers1,0984
Water9,782543
1
A: STEROID DELTA-ISOMERASE
B: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3954
Polymers26,8462
Non-polymers5492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-7 kcal/mol
Surface area12320 Å2
MethodPISA
2
C: STEROID DELTA-ISOMERASE
D: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3954
Polymers26,8462
Non-polymers5492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint1.2 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.353, 95.352, 60.402
Angle α, β, γ (deg.)90.00, 91.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
STEROID DELTA-ISOMERASE / DELTA-5-3-KETOSTEROID ISOMERASE


Mass: 13423.171 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS TESTOSTERONI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical
ChemComp-ESR / 5-ALPHA-ESTRAN-3,17-DIONE / (13S)-13-METHYLDODECAHYDRO-1H-CYCLOPENTA[A]PHENANTHRENE-3,17(2H,4H)-DIONE


Mass: 274.398 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H26O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: A 3-OXO-DELTA(5)-STEROID = A 3-OXO- DELTA(4)-STEROID. ENGINEERED RESIDUE IN ...CATALYTIC ACTIVITY: A 3-OXO-DELTA(5)-STEROID = A 3-OXO- DELTA(4)-STEROID. ENGINEERED RESIDUE IN CHAIN A, ASP 38 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 38 TO ASN ENGINEERED RESIDUE IN CHAIN C, ASP 38 TO ASN ENGINEERED RESIDUE IN CHAIN D, ASP 38 TO ASN

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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: 2.1 Å3/Da / Density % sol: 39.8 %
Crystal growpH: 4.6
Details: PEG 4K 24%, 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: Nov 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 1.53→30 Å / Num. obs: 67193 / % possible obs: 94.1 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 34.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.53→30 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3151 5 %RANDOM
Rwork0.203 ---
obs0.203 62322 93.3 %-
Refinement stepCycle: LAST / Resolution: 1.53→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 80 543 4407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.203
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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