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- PDB-6wkf: Crystal structure of pentalenene synthase mutant F76Y complexed w... -

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Basic information

Entry
Database: PDB / ID: 6wkf
TitleCrystal structure of pentalenene synthase mutant F76Y complexed with 12,13-difluorofarnesyl diphosphate
ComponentsPentalenene synthase
KeywordsMETAL BINDING PROTEIN / LYASE/INHIBITOR / Terpene synthase / terpene synthase fold / sesquiterpene / fluoro analog / metal binding / LYASE-INHIBITOR complex
Function / homology
Function and homology information


pentalenene synthase / pentalenene synthase activity / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
: / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-FDF / Pentalenene synthase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 16, 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)76,5513
Polymers76,1332
Non-polymers4181
Water1,74797
1
A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4852
Polymers38,0661
Non-polymers4181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase


Theoretical massNumber of molelcules
Total (without water)38,0661
Polymers38,0661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.267, 183.267, 56.728
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-FDF / (2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate


Mass: 418.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26F2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.61 Å3/Da / Density % sol: 65.95 %
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: 0.97 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: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 38010 / % possible obs: 99.8 % / Redundancy: 19.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5514 / % 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: 2.5→19.996 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.94
RfactorNum. reflection% reflection
Rfree0.235 1865 4.93 %
Rwork0.2076 --
obs0.2089 37825 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.95 Å2 / Biso mean: 68.9834 Å2 / Biso min: 38.25 Å2
Refinement stepCycle: final / Resolution: 2.5→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4430 0 26 97 4553
Biso mean--92.36 63.78 -
Num. residues----572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034560
X-RAY DIFFRACTIONf_angle_d0.5136199
X-RAY DIFFRACTIONf_dihedral_angle_d18.9822716
X-RAY DIFFRACTIONf_chiral_restr0.036663
X-RAY DIFFRACTIONf_plane_restr0.003820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.56750.29881570.2662270899
2.5675-2.64290.36521360.2661270499
2.6429-2.7280.28911310.2539276199
2.728-2.82520.2791880.2482270799
2.8252-2.9380.25091050.2425274699
2.938-3.07130.31561370.24472780100
3.0713-3.23260.3071290.24582752100
3.2326-3.43410.24611430.23812770100
3.4341-3.69780.24121430.20682772100
3.6978-4.06710.19761460.19062801100
4.0671-4.64910.22481460.18272765100
4.6491-5.83320.20311370.19642830100
5.8332-19.9960.21061670.18492864100

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