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- PDB-1e3r: Crystal structure of ketosteroid isomerase mutant D40N (D38N TI n... -

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Basic information

Entry
Database: PDB / ID: 1e3r
TitleCrystal structure of ketosteroid isomerase mutant D40N (D38N TI numbering) from Pseudomonas putida complexed with androsten-3beta-ol-17-one
ComponentsISOMERASE
KeywordsISOMERASE / KSI KETOSTEROIED ISOMERASE / LBHB / ANDROSTEN-3BETA-OL-17-ONE
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
3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHa, N.-C. / Kim, M.-S. / Hyun, B.-H. / Oh, B.-H.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Detection of Large Pka Perturbations of an Inhibitor and a Catalytic Group at an Enzyme Active Site, a Mechanistic Basis for Catalytic Power of Many Enzymes
Authors: Ha, N.-C. / Kim, M.-S. / Lee, W. / Choi, K.Y. / Oh, B.-H.
History
DepositionJun 22, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2001Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOMERASE
B: ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6724
Polymers29,0952
Non-polymers5772
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)85.900, 72.370, 50.530
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ISOMERASE / / KSI


Mass: 14547.515 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ANDROSTENE-3BETA-OL-17-ONE / Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P07445
#2: Chemical ChemComp-AND / 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / Dehydroepiandrosterone


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION ASP40ASN

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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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop / Details: Kim, S.W., (1997) Biochemistry, 36, 14030.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.1 Msodium acetate1reservoir
20.1 Mammonium acetate1reservoir
320 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 11746 / % possible obs: 82.2 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 66.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3R

Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.279 -5 %RANDOM
Rwork0.193 ---
obs0.193 10870 83.5349 %-
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 42 76 2062
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_deg1.323
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

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