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- PDB-6f53: CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE QUADRUPLE VARIANT V88I... -

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Basic information

Entry
Database: PDB / ID: 6f53
TitleCRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE QUADRUPLE VARIANT V88I/L99V/D103S/V101A
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: 1.49 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

Downloads & links

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Assembly

Deposited unit
A: Steroid Delta-isomerase


Theoretical massNumber of molelcules
Total (without water)13,7361
Polymers13,7361
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.740, 94.720, 73.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-261-

HOH

21A-264-

HOH

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Components

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


Mass: 13735.584 Da / Num. of mol.: 1
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.: 86 / 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: 45.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging 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: 1.49→29.1 Å / Num. obs: 20641 / % possible obs: 99.6 % / Redundancy: 5.8 % / Net I/σ(I): 23.1
Reflection shellResolution: 1.49→1.55 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 1.49→19.92 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.12
RfactorNum. reflection% reflection
Rfree0.2021 1055 5.11 %
Rwork0.1828 --
obs0.1838 20641 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.99 Å2 / Biso mean: 33.786 Å2 / Biso min: 15.92 Å2
Refinement stepCycle: final / Resolution: 1.49→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 0 86 1046
Biso mean---41.79 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007981
X-RAY DIFFRACTIONf_angle_d1.0791331
X-RAY DIFFRACTIONf_chiral_restr0.042142
X-RAY DIFFRACTIONf_plane_restr0.006179
X-RAY DIFFRACTIONf_dihedral_angle_d14.303359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.55780.3171080.3072373248198
1.5578-1.63990.29251270.26852404253198
1.6399-1.74260.24091420.20962405254799
1.7426-1.87710.20611400.18352446258699
1.8771-2.06580.1941460.167924282574100
2.0658-2.36430.19541270.1712472259999
2.3643-2.97720.19581300.191425012631100
2.9772-19.92130.18841350.16762557269298
Refinement TLS params.Method: refined / Origin x: -5.7173 Å / Origin y: -11.7271 Å / Origin z: -1.3705 Å
111213212223313233
T0.2176 Å20.0024 Å2-0.0038 Å2-0.1812 Å2-0.0065 Å2--0.1917 Å2
L0.9859 °20.2163 °20.4208 °2-1.3475 °2-0.5732 °2--1.0843 °2
S0.0485 Å °0.031 Å °-0.0539 Å °-0.1321 Å °-0.0119 Å °-0.0143 Å °0.2917 Å °-0.0034 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 127
2X-RAY DIFFRACTION1allS1 - 86

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