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- PDB-6f50: CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE DOUBLE VARIANT V88I/L99V -

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Basic information

Entry
Database: PDB / ID: 6f50
TitleCRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE DOUBLE VARIANT V88I/L99V
ComponentsSteroid Delta-isomerase
KeywordsISOMERASE / Ksi
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 / Resolution: 2 Å
AuthorsDunstan, M. / Currin, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: ACS Catal / Year: 2018
Title: Engineering the "Missing Link" in Biosynthetic (-)-Menthol Production: Bacterial Isopulegone Isomerase.
Authors: Currin, A. / Dunstan, M.S. / Johannissen, L.O. / Hollywood, K.A. / Vinaixa, M. / Jervis, A.J. / Swainston, N. / Rattray, N.J.W. / Gardiner, J.M. / Kell, D.B. / Takano, E. / Toogood, H.S. / Scrutton, N.S.
History
DepositionNov 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)27,5832
Polymers27,5832
Non-polymers00
Water2,882160
1
A: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)13,7921
Polymers13,7921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)13,7921
Polymers13,7921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.692, 73.539, 95.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Steroid Delta-isomerase / Delta(5)-3-ketosteroid isomerase


Mass: 13791.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10-25% PEG3350 with 0.2 M MgCl2; ii) 10-25% PEG3350 with 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→95.4 Å / Num. obs: 17276 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.1 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 2→29.192 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.2271 835 4.83 %
Rwork0.1832 --
obs0.1854 17276 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.11 Å2 / Biso mean: 32.9813 Å2 / Biso min: 10.87 Å2
Refinement stepCycle: final / Resolution: 2→29.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 0 160 2088
Biso mean---38.67 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091970
X-RAY DIFFRACTIONf_angle_d1.0482674
X-RAY DIFFRACTIONf_chiral_restr0.044286
X-RAY DIFFRACTIONf_plane_restr0.005360
X-RAY DIFFRACTIONf_dihedral_angle_d14.959722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.12530.26861270.19972641276896
2.1253-2.28940.24921530.18682628278197
2.2894-2.51960.24221320.18462728286098
2.5196-2.88390.24481490.18932718286799
2.8839-3.63240.22711220.1862800292299
3.6324-29.19470.20261520.17442926307899
Refinement TLS params.Method: refined / Origin x: -5.8702 Å / Origin y: -18.4632 Å / Origin z: 23.9284 Å
111213212223313233
T0.0936 Å2-0.0002 Å20.0114 Å2-0.0936 Å20.0053 Å2--0.1198 Å2
L0.8269 °20.0701 °2-0.1383 °2-0.8674 °20.0832 °2--1.7996 °2
S-0.0127 Å °0.0267 Å °-0.031 Å °-0.0955 Å °0.0197 Å °-0.0102 Å °-0.003 Å °0.0192 Å °-0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 127
2X-RAY DIFFRACTION1allB3 - 127
3X-RAY DIFFRACTION1allS1 - 160

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