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- PDB-6wkj: Crystal structure of pentalenene synthase mutant F76H complexed w... -

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Basic information

Entry
Database: PDB / ID: 6wkj
TitleCrystal structure of pentalenene synthase mutant F76H 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: 2.3 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 9, 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)76,5013
Polymers76,0832
Non-polymers4181
Water3,819212
1
A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4602
Polymers38,0411
Non-polymers4181
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)182.026, 182.026, 56.425
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: 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: 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.: 212 / 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: 3.55 Å3/Da / Density % sol: 65.32 %
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: 0.97 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: 2.3→20 Å / Num. obs: 47794 / % possible obs: 99.8 % / Redundancy: 19.9 % / CC1/2: 1 / Rmerge(I) obs: 0.109 / Net I/σ(I): 20
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 20.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6918 / % 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→19.985 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.12
RfactorNum. reflection% reflection
Rfree0.2464 2425 5.08 %
Rwork0.2113 --
obs0.2132 47769 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.65 Å2 / Biso mean: 59.9716 Å2 / Biso min: 27.67 Å2
Refinement stepCycle: final / Resolution: 2.3→19.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 26 213 4588
Biso mean--108.57 59.03 -
Num. residues----555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044488
X-RAY DIFFRACTIONf_angle_d0.6056099
X-RAY DIFFRACTIONf_dihedral_angle_d18.5912683
X-RAY DIFFRACTIONf_chiral_restr0.039647
X-RAY DIFFRACTIONf_plane_restr0.004808
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3-2.34690.33891110.28772668
2.3469-2.39790.32251390.27442632
2.3979-2.45350.34581390.26352668
2.4535-2.51480.32671580.26282613
2.5148-2.58260.29191410.24172674
2.5826-2.65850.2751130.24772665
2.6585-2.74410.29411370.24692640
2.7441-2.84190.28221240.24212706
2.8419-2.95530.27871230.2412657
2.9553-3.08940.27281560.24232643
3.0894-3.25160.2981530.23772651
3.2516-3.45430.29861510.2262666
3.4543-3.71950.26111600.19712660
3.7195-4.09090.1891560.18242651
4.0909-4.67620.18711630.17262684
4.6762-5.86670.21441540.19422679
5.8667-19.9850.24531470.20152787

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