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- PDB-6wkh: Crystal structure of pentalenene synthase mutant F76W complexed w... -

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Basic information

Entry
Database: PDB / ID: 6wkh
TitleCrystal structure of pentalenene synthase mutant F76W 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: 2.55 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

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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)76,5973
Polymers76,1792
Non-polymers4181
Water1,820101
1
A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5082
Polymers38,0891
Non-polymers4181
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)185.019, 185.019, 56.930
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: 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: 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.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.69 Å3/Da / Density % sol: 66.69 %
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: 2.55→20 Å / Num. obs: 36655 / % possible obs: 99.8 % / Redundancy: 19.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.137 / Net I/σ(I): 15.9
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.67 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5340 / % 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: 2.55→19.886 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 1853 5.06 %
Rwork0.2253 34785 -
obs0.2269 36638 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.81 Å2 / Biso mean: 72.7236 Å2 / Biso min: 34.97 Å2
Refinement stepCycle: final / Resolution: 2.55→19.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 0 26 101 4504
Biso mean--108.14 64.25 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024511
X-RAY DIFFRACTIONf_angle_d0.3966134
X-RAY DIFFRACTIONf_dihedral_angle_d18.1422679
X-RAY DIFFRACTIONf_chiral_restr0.034653
X-RAY DIFFRACTIONf_plane_restr0.003809
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.55-2.61880.35161210.29432695
2.6188-2.69570.3381490.28322636
2.6957-2.78250.36891410.2772629
2.7825-2.88160.32181370.25812668
2.8816-2.99660.29051400.25342668
2.9966-3.13250.24861480.2542642
3.1325-3.2970.30431330.24492681
3.297-3.50250.27761610.24082643
3.5025-3.77120.29321470.22672665
3.7712-4.14770.25111540.21062657
4.1477-4.74070.20721230.20362734
4.7407-5.94620.23611690.21532663
5.9462-19.8860.22221300.20612804

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