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- PDB-6wkc: Crystal structure of pentalenene synthase complexed with Mg2+ ions -

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Basic information

Entry
Database: PDB / ID: 6wkc
TitleCrystal structure of pentalenene synthase complexed with Mg2+ ions
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: 1.65 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)76,1986
Polymers76,1012
Non-polymers974
Water21,0961171
1
A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0993
Polymers38,0501
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0993
Polymers38,0501
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.659, 73.745, 81.224
Angle α, β, γ (deg.)90.000, 100.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 38050.414 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1171 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 8-14% PEG4000, 100 mM HEPES, 200 mM MgCl2, 15% ethylene glycol and 10% 2-propanol
PH range: 6.5 - 7.5

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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: Sep 28, 2018 / 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: 1.65→20 Å / Num. obs: 83734 / % possible obs: 98.9 % / Redundancy: 6.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2 / Num. unique obs: 12092 / CC1/2: 0.72 / % possible all: 98

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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: 1.65→19.986 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.8
RfactorNum. reflection% reflection
Rfree0.1929 4157 4.97 %
Rwork0.1668 --
obs0.1681 83593 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.62 Å2 / Biso mean: 21.7471 Å2 / Biso min: 9.03 Å2
Refinement stepCycle: final / Resolution: 1.65→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 4 1186 5998
Biso mean--23.27 33.57 -
Num. residues----606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054971
X-RAY DIFFRACTIONf_angle_d0.7896766
X-RAY DIFFRACTIONf_dihedral_angle_d17.0072980
X-RAY DIFFRACTIONf_chiral_restr0.044710
X-RAY DIFFRACTIONf_plane_restr0.005908
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.66870.29891390.2487258998
1.6687-1.68840.28231490.2404263097
1.6884-1.70890.23361440.2336259699
1.7089-1.73060.25081400.2169262897
1.7306-1.75330.22351440.2198259898
1.7533-1.77730.27031400.2082261198
1.7773-1.80270.23691500.1942261898
1.8027-1.82960.22221260.1934263998
1.8296-1.85820.24651350.1982263898
1.8582-1.88860.22961340.2145264198
1.8886-1.92110.41171390.2854255097
1.9211-1.9560.24541440.2109263898
1.956-1.99360.18221260.181268599
1.9936-2.03430.19181320.177264399
2.0343-2.07850.23551380.188260398
2.0785-2.12680.20441240.155264099
2.1268-2.17990.18921300.1596266099
2.1799-2.23880.18521310.1767267098
2.2388-2.30460.21261320.1789258797
2.3046-2.37880.18961300.1487269299
2.3788-2.46370.21171330.1521263699
2.4637-2.56210.18861500.1538266399
2.5621-2.67850.1791380.1605267199
2.6785-2.81930.20041340.16282684100
2.8193-2.99540.18121490.15732680100
2.9954-3.22580.17331260.15582712100
3.2258-3.54880.15181450.14272699100
3.5488-4.05860.14751520.12962685100
4.0586-5.09940.14061580.13572697100
5.0994-19.9860.19631450.1742753100

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