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- PDB-1qjg: Crystal structure of delta5-3-ketosteroid isomerase from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 1qjg
TitleCrystal structure of delta5-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin
ComponentsKETOSTEROID ISOMERASE
KeywordsISOMERASE / KETOSTEROID ISOMERASE / KSI / 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
EQUILENIN / Steroid Delta-isomerase
Similarity search - Component
Biological speciesPSEUDOMONAS TESTOSTERONI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCho, H.-S. / Oh, B.-H.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal Structure of Delta-5-3-Ketosteroid Isomerase from Pseudomonas Testosteroni in Complex with Equilenin Settles the Correct Hydrogen Scheme for Transition-State Stabilization
Authors: Cho, H.-S. / Ha, N.-C. / Choi, G. / Kim, H.-J. / Lee, D. / Oh, K.S. / Kim, K.S. / Lee, W. / Choi, K.Y. / Oh, B.-H.
#1: Journal: Biochemistry / Year: 1998
Title: Crystal Structure of Delta-Ketosteroid Isomerase from Pseudomonas Testosteroni.
Authors: Cho, H.-S. / Choi, G. / Choi, K.Y. / Oh, B.-H.
History
DepositionJun 24, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KETOSTEROID ISOMERASE
B: KETOSTEROID ISOMERASE
C: KETOSTEROID ISOMERASE
D: KETOSTEROID ISOMERASE
E: KETOSTEROID ISOMERASE
F: KETOSTEROID ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,23313
Polymers80,5396
Non-polymers1,6947
Water2,792155
1
C: KETOSTEROID ISOMERASE
D: KETOSTEROID ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3794
Polymers26,8462
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-7.9 kcal/mol
Surface area11960 Å2
MethodPISA
2
A: KETOSTEROID ISOMERASE
B: KETOSTEROID ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4755
Polymers26,8462
Non-polymers6293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-14.4 kcal/mol
Surface area11480 Å2
MethodPISA
3
E: KETOSTEROID ISOMERASE
F: KETOSTEROID ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3794
Polymers26,8462
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-5.2 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.900, 72.500, 80.800
Angle α, β, γ (deg.)90.00, 104.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE ASYMMETRIC UNIT CONTAINS 3 INDEPENDENT COPIES OF THEBIOMOLECULE WHICH CONSISTS OF A HOMO -DIMERIC-COMPLEX

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Components

#1: Protein
KETOSTEROID ISOMERASE


Mass: 13423.171 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: EQUILENIN, SO4 / Source: (gene. exp.) PSEUDOMONAS TESTOSTERONI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00947
#2: Chemical
ChemComp-EQU / EQUILENIN / Equilenin


Mass: 266.334 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H18O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 60 %
Crystal growpH: 4.6
Details: PEG 4000 25%, 0.1M SODIUM ACETATE, PH 4.6, 0.2M AMMONIUM SULFATE
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
225 %PEG40001drop
30.1 Msodium acetate1drop
40.2 Mammonium sulfate1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→20 Å / Num. obs: 37500 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Rsym value: 0.069
Reflection shellResolution: 2.26→2.34 Å / % possible all: 90
Reflection
*PLUS
Num. measured all: 102917 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8CHO

8cho


Resolution: 2.3→10 Å / 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. atoms5666 0 125 155 5946
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_deg1.53
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_d1.389
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 / Version: 3 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.389
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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