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- PDB-1dmn: CRYSTAL STRUCTURE OF MUTANT ENZYME Y32F/Y57F OF KETOSTEROID ISOME... -

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Basic information

Entry
Database: PDB / ID: 1dmn
TitleCRYSTAL STRUCTURE OF MUTANT ENZYME Y32F/Y57F OF KETOSTEROID ISOMERASE FROM PSEUDOMONAS PUTIDA BIOTYPE B
ComponentsSTEROID DELTA-ISOMERASE
KeywordsISOMERASE / CONESHELL / CLOSED BARREL / CURVED B-SHEET
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
Steroid Delta-isomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.05 Å
AuthorsKim, D.H. / Jang, D.S. / Nam, G.H. / Oh, B.H. / Choi, K.Y.
Citation
Journal: Biochemistry / Year: 2000
Title: Contribution of the hydrogen-bond network involving a tyrosine triad in the active site to the structure and function of a highly proficient ketosteroid isomerase from Pseudomonas putida biotype B.
Authors: Kim, D.H. / Jang, D.S. / Nam, G.H. / Choi, G. / Kim, J.S. / Ha, N.C. / Kim, M.S. / Oh, B.H. / Choi, K.Y.
#1: Journal: Biochemistry / Year: 1997
Title: High-Resolution Crystal Structures of delta(5)-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.
#2: 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.
#3: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of delta(5)-3-Ketosteroid Isomerase from Pseudomonas testosteroni in Complex with Equilenin Settles the Correct Hydrogen Bonding 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.
History
DepositionDec 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STEROID DELTA-ISOMERASE


Theoretical massNumber of molelcules
Total (without water)14,5171
Polymers14,5171
Non-polymers00
Water86548
1
A: STEROID DELTA-ISOMERASE

A: STEROID DELTA-ISOMERASE


Theoretical massNumber of molelcules
Total (without water)29,0332
Polymers29,0332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)36.36, 96.48, 74.60
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein STEROID DELTA-ISOMERASE


Mass: 14516.501 Da / Num. of mol.: 1 / Mutation: Y32F, Y57F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: SODIUM ACETATE, AMMONIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.0 Msodium acetate1reservoir
20.1 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 9209 / Num. obs: 8592 / % possible obs: 93.3 % / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 0.5 / Redundancy: 5.5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.22 / % possible all: 89

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.05→20 Å / σ(F): 0.5 / σ(I): 0.5 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.244 430 5%
Rwork0.195 --
all0.195 9209 -
obs0.195 8592 -
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 0 48 1003
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.03
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
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0.5 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.2 Å2

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