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- PDB-8cho: CRYSTAL STRUCTURE OF DELTA5-3-KETOSTEROID ISOMERASE FROM PSEUDOMO... -

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Basic information

Entry
Database: PDB / ID: 8cho
TitleCRYSTAL STRUCTURE OF DELTA5-3-KETOSTEROID ISOMERASE FROM PSEUDOMONAS TESTOSTERONI
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE / STEROID ISOMERATION
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 domain / Nuclear transport factor 2 (NTF2) 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
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / Steroid Delta-isomerase
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsCho, H.-S. / Oh, B.-H.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structure and enzyme mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni.
Authors: Cho, H.S. / Choi, G. / Choi, K.Y. / Oh, B.H.
#1: Journal: Biochemistry / Year: 1998
Title: Erratum. 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
DepositionJan 6, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)13,7492
Polymers13,4241
Non-polymers3241
Water43224
1
A: STEROID DELTA-ISOMERASE
hetero molecules

A: STEROID DELTA-ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4974
Polymers26,8482
Non-polymers6492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)61.680, 61.680, 143.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein STEROID DELTA-ISOMERASE /


Mass: 13424.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Comamonas testosteroni (bacteria) / References: UniProt: P00947, steroid Delta-isomerase
#2: Chemical ChemComp-P4C / O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL / POLYETHYLENE 400


Mass: 324.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.95 Å3/Da / Density % sol: 58 %
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.3 Mammonium sulfate1reservoir
23-5 %PEG4001reservoir
30.1 MHEPES1reservoir
45 mg/mlprotein1drop

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Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 95 %

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3.2refinement
X-PLOR3phasing
RefinementResolution: 2.3→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.271 366 5 %RANDOM
Rwork0.205 ---
obs0.205 7337 95 %-
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 22 24 1197
Software
*PLUS
Name: X-PLOR / Version: 3.2 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 1 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_d1.615

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