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- PDB-6wke: Crystal structure of pentalenene synthase mutant F76Y -

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Basic information

Entry
Database: PDB / ID: 6wke
TitleCrystal structure of pentalenene synthase mutant F76Y
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 / Isoprenoid synthase domain superfamily / antibiotic biosynthetic process / metal ion binding / Pentalenene synthase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pentalenene synthase
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2253
Polymers76,1332
Non-polymers921
Water4,216234
1
A: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)38,0661
Polymers38,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1592
Polymers38,0661
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.781, 181.781, 56.389
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 38066.410 Da / Num. of mol.: 2 / Mutation: F76Y
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.53 Å3/Da / Density % sol: 65.18 %
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: Aug 16, 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: 2.4→20 Å / Num. obs: 41985 / % possible obs: 99.8 % / Redundancy: 20.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.128 / Net I/σ(I): 21.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 21.1 % / Rmerge(I) obs: 1.52 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6084 / CC1/2: 0.76 / % 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: 2.4→19.965 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2321 2118 5.05 %
Rwork0.1979 39853 -
obs0.1996 41971 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.26 Å2 / Biso mean: 56.5233 Å2 / Biso min: 27.55 Å2
Refinement stepCycle: final / Resolution: 2.4→19.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 6 234 4734
Biso mean--85.17 56.87 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034607
X-RAY DIFFRACTIONf_angle_d0.5136262
X-RAY DIFFRACTIONf_dihedral_angle_d19.7162758
X-RAY DIFFRACTIONf_chiral_restr0.037668
X-RAY DIFFRACTIONf_plane_restr0.004834
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4001-2.45580.31871270.26162675
2.4558-2.51710.29481460.26472608
2.5171-2.5850.32011580.24622603
2.585-2.66090.29321250.24472647
2.6609-2.74660.29391410.23762635
2.7466-2.84450.30481530.23422640
2.8445-2.9580.27461430.23272640
2.958-3.09220.32781300.23212644
3.0922-3.25460.28181320.22272660
3.2546-3.45750.24121620.20862636
3.4575-3.72290.20431350.17872671
3.7229-4.09460.21151310.16962653
4.0946-4.68040.19541430.16232692
4.6804-5.87180.20141510.18232677
5.8718-19.9650.18621410.18882772

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