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- PDB-6wki: Crystal structure of pentalenene synthase mutant F76H -

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Basic information

Entry
Database: PDB / ID: 6wki
TitleCrystal structure of pentalenene synthase mutant F76H
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: 2.35 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 23, 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)76,0832
Polymers76,0832
Non-polymers00
Water3,117173
1
A: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)38,0411
Polymers38,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)38,0411
Polymers38,0411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)181.543, 181.543, 56.471
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: 38041.387 Da / Num. of mol.: 2 / Mutation: F76H
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.: 173 / 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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
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: 2.35→20 Å / Num. obs: 44617 / % possible obs: 99.8 % / Redundancy: 20.4 % / Biso Wilson estimate: 52.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.111 / Net I/σ(I): 23.5
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.79 / Mean I/σ(I) obs: 2 / Num. unique obs: 6448 / CC1/2: 0.708 / % 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: 2.35→19.97 Å / SU ML: 0.3012 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5767
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2408 2165 4.85 %
Rwork0.2198 42436 -
obs0.2208 44601 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.13 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 0 0 173 4659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00154606
X-RAY DIFFRACTIONf_angle_d0.41856264
X-RAY DIFFRACTIONf_chiral_restr0.0342666
X-RAY DIFFRACTIONf_plane_restr0.0032834
X-RAY DIFFRACTIONf_dihedral_angle_d17.52782747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.32091340.30642802X-RAY DIFFRACTION100
2.4-2.460.3721360.29722801X-RAY DIFFRACTION100
2.46-2.530.32511620.29712783X-RAY DIFFRACTION100
2.53-2.610.341160.28262844X-RAY DIFFRACTION100
2.61-2.690.33381440.28012821X-RAY DIFFRACTION100
2.69-2.790.25491230.27282833X-RAY DIFFRACTION100
2.79-2.90.32481460.26252788X-RAY DIFFRACTION100
2.9-3.030.30871340.26532840X-RAY DIFFRACTION100
3.03-3.190.30091450.26192820X-RAY DIFFRACTION100
3.19-3.390.27411600.24312793X-RAY DIFFRACTION100
3.39-3.650.23421480.22162832X-RAY DIFFRACTION100
3.65-4.010.21291710.19392830X-RAY DIFFRACTION100
4.01-4.580.20311620.18192818X-RAY DIFFRACTION100
4.58-5.750.18871360.19262892X-RAY DIFFRACTION100
5.75-19.970.20991480.18992939X-RAY DIFFRACTION99.84

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