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- PDB-6q4s: Crystal structure of a-eudesmol synthase -

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Basic information

Entry
Database: PDB / ID: 6q4s
TitleCrystal structure of a-eudesmol synthase
ComponentsPentalenene synthase
KeywordsUNKNOWN FUNCTION / Sesquiterpene / terpene synthase / PLANT PROTEIN
Function / homology: / Lyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / : / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / Terpene synthase
Function and homology information
Biological speciesStreptomyces chartreusis NRRL 3882 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsCorreia Cordeiro, R.S. / Hakansson, M. / Logan, D.T. / Kourist, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Commission634200 Germany
CitationJournal: J.Biotechnol. / Year: 2019
Title: Discovery of three novel sesquiterpene synthases from Streptomyces chartreusis NRRL 3882 and crystal structure of an alpha-eudesmol synthase.
Authors: Kracht, O.N. / Correia Cordeiro, R.S. / Hakansson, M. / Stockmann, J. / Sander, D. / Bandow, J. / Senges, C.H.R. / Logan, D.T. / Kourist, R.
History
DepositionDec 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 24, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5345
Polymers39,3921
Non-polymers1424
Water3,297183
1
A: Pentalenene synthase
hetero molecules

A: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,06810
Polymers78,7852
Non-polymers2848
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area3980 Å2
ΔGint-80 kcal/mol
Surface area26220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.140, 103.140, 139.665
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Pentalenene synthase / 7-epi-a-eudesmol synthase


Mass: 39392.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces chartreusis NRRL 3882 (bacteria)
Gene: penA, SCNRRL3882_7461 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N9BKY0, pentalenene synthase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M MgCl2, 10% (v/v) propan-2-ol, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.83→48.38 Å / Num. obs: 38890 / % possible obs: 99.5 % / Redundancy: 10.4 % / CC1/2: 1 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.962 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3646 / CC1/2: 0.586 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1


Resolution: 1.83→48.38 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.504 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 1928 5 %RANDOM
Rwork0.19673 ---
obs0.1991 36547 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.778 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.83→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 4 183 2697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192591
X-RAY DIFFRACTIONr_bond_other_d0.0020.022378
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9273516
X-RAY DIFFRACTIONr_angle_other_deg1.07135431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5785310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03922.183142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33115418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2951534
X-RAY DIFFRACTIONr_chiral_restr0.1150.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212972
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02668
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0074.1661240
X-RAY DIFFRACTIONr_mcbond_other4.0024.1631239
X-RAY DIFFRACTIONr_mcangle_it5.3566.2121550
X-RAY DIFFRACTIONr_mcangle_other5.3576.2171551
X-RAY DIFFRACTIONr_scbond_it4.884.7211351
X-RAY DIFFRACTIONr_scbond_other4.8784.7241352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.096.881967
X-RAY DIFFRACTIONr_long_range_B_refined8.96648.6143087
X-RAY DIFFRACTIONr_long_range_B_other8.97448.3753051
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.834→1.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 126 -
Rwork0.38 2594 -
obs--96.15 %

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