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- PDB-6wkg: Crystal structure of pentalenene synthase mutant F76W -

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Basic information

Entry
Database: PDB / ID: 6wkg
TitleCrystal structure of pentalenene synthase mutant F76W
ComponentsPentalenene synthase
KeywordsMETAL BINDING PROTEIN / LYASE / Terpene synthase / terpene synthase fold / sesquiterpene / fluoro analog / metal binding
Function / homologypentalenene synthase / pentalenene synthase activity / Terpene cyclase-like 2 / : / Terpene synthase family 2, C-terminal metal binding / antibiotic biosynthetic process / Isoprenoid synthase domain superfamily / metal ion binding / Pentalenene synthase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPrem Kumar, R. / Matos, J.O. / Oprian, D.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007596 United States
CitationJournal: Biochemistry / Year: 2020
Title: Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase.
Authors: Matos, J.O. / Kumar, R.P. / Ma, A.C. / Patterson, M. / Krauss, I.J. / Oprian, D.D.
History
DepositionApr 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pentalenene synthase
B: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)76,1792
Polymers76,1792
Non-polymers00
Water5,477304
1
A: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)38,0891
Polymers38,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)38,0891
Polymers38,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.151, 183.151, 56.512
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c

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Components

#1: Protein Pentalenene synthase / PS / Pentalenolactone biosynthesis protein A / Sesquiterpene cyclase / Sesquiterpene synthase


Mass: 38089.445 Da / Num. of mol.: 2 / Mutation: F76W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Gene: penA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q55012, pentalenene synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8-1.2 M sodium tartrate, 100 mM Tris, and 5 mM DTT
PH range: 7.5 - 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2019 / Details: Mirrors
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 48511 / % possible obs: 99.8 % / Redundancy: 19.6 % / Biso Wilson estimate: 44.72 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.136 / Net I/σ(I): 16.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.46 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7097 / CC1/2: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1


Resolution: 2.3→19.98 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.246
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2366 2370 4.89 %
Rwork0.2155 46129 -
obs0.2165 48499 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.62 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4455 0 0 304 4759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00174563
X-RAY DIFFRACTIONf_angle_d0.42786199
X-RAY DIFFRACTIONf_chiral_restr0.0349664
X-RAY DIFFRACTIONf_plane_restr0.003816
X-RAY DIFFRACTIONf_dihedral_angle_d18.1072726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.26181520.25432738X-RAY DIFFRACTION100
2.35-2.40.30041530.26472657X-RAY DIFFRACTION100
2.4-2.450.29371510.24652670X-RAY DIFFRACTION100
2.45-2.510.27671380.25472688X-RAY DIFFRACTION100
2.51-2.580.271350.23572708X-RAY DIFFRACTION100
2.58-2.660.25861320.23632692X-RAY DIFFRACTION100
2.66-2.740.29731310.24052688X-RAY DIFFRACTION100
2.74-2.840.28511240.22992721X-RAY DIFFRACTION100
2.84-2.960.24571310.23162719X-RAY DIFFRACTION100
2.96-3.090.25651430.22882689X-RAY DIFFRACTION100
3.09-3.250.27151230.2352708X-RAY DIFFRACTION100
3.25-3.450.27831270.22562721X-RAY DIFFRACTION100
3.45-3.720.21581450.20482713X-RAY DIFFRACTION99.97
3.72-4.090.19671400.19572722X-RAY DIFFRACTION100
4.09-4.680.17861450.19252745X-RAY DIFFRACTION100
4.68-5.870.20831580.20112714X-RAY DIFFRACTION100
5.87-19.980.26151420.20842836X-RAY DIFFRACTION100

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