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- PDB-1vzz: CRYSTAL STRUCTURE OF MUTANT ENZYME Y32F/D103L OF KETOSTEROID ISOM... -

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Basic information

Entry
Database: PDB / ID: 1vzz
TitleCRYSTAL STRUCTURE OF MUTANT ENZYME Y32F/D103L 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJang, D.S. / Cha, H.J. / Choi, K.Y.
Citation
Journal: Biochem.J. / Year: 2004
Title: Structural Double-Mutant Cycle Analysis of a Hydrogen Bond Network in Ketosteroid Isomerase from Pseudomonas Putida Biotype B.
Authors: Jang, D.S. / Cha, H.J. / Cha, S.S. / Hong, B.H. / Ha, N.C. / Lee, J.Y. / Oh, B.H. / Lee, H.S. / Choi, K.Y.
#1: Journal: Biochemistry / Year: 2000
Title: Contribution of the Hydrogen Bond Network Involving a Tyrosine Triad in the Active Site to 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.D. / Kim, J.S. / Ha, N.C. / Kim, M.S. / Oh, B.H. / Choi, K.Y.
History
DepositionMay 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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Assembly

Deposited unit
A: STEROID DELTA-ISOMERASE
B: STEROID DELTA-ISOMERASE


Theoretical massNumber of molelcules
Total (without water)29,0612
Polymers29,0612
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.279, 72.958, 95.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14530.571 Da / Num. of mol.: 2 / Mutation: YES
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.: 88 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUES CHAINS A, B : TYR (32) PHE, ASP (103) LEU

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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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growpH: 4.6 / Details: SODIUM ACETATE, AMMONIUM ACETATE, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 5, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 6746 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 6.3
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.226 / % possible all: 82.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DMQ

1dmq


Resolution: 2.3→28.41 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2640441.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1129 10 %RANDOM
Rwork0.227 ---
obs0.227 11268 97.5 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.379582 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.56 Å20 Å20 Å2
2---1.28 Å20 Å2
3----5.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 0 88 1977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
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
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 186 10.1 %
Rwork0.213 1649 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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