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- PDB-5nx6: Crystal structure of 1,8-cineole synthase from Streptomyces clavu... -

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Basic information

Entry
Database: PDB / ID: 5nx6
TitleCrystal structure of 1,8-cineole synthase from Streptomyces clavuligerus in complex with 2-fluoroneryl diphosphate
ComponentsPentalenene synthase
KeywordsLYASE / terpene synthase / 1 / 8-cineole / monoterpenoid / Eucalyptol
Function / homology
Function and homology information


1,8-cineole synthase / 1,8-cineole synthase activity / geranyl diphosphate metabolic process / magnesium 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
2-ethyl-2-(hydroxymethyl)propane-1,3-diol / Chem-LA6 / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE / 1,8-cineole synthase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsKaruppiah, V. / Leys, D. / Scrutton, N.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M000354/1 United Kingdom
CitationJournal: ACS Catal / Year: 2017
Title: Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.
Authors: Karuppiah, V. / Ranaghan, K.E. / Leferink, N.G.H. / Johannissen, L.O. / Shanmugam, M. / Ni Cheallaigh, A. / Bennett, N.J. / Kearsey, L.J. / Takano, E. / Gardiner, J.M. / van der Kamp, M.W. / ...Authors: Karuppiah, V. / Ranaghan, K.E. / Leferink, N.G.H. / Johannissen, L.O. / Shanmugam, M. / Ni Cheallaigh, A. / Bennett, N.J. / Kearsey, L.J. / Takano, E. / Gardiner, J.M. / van der Kamp, M.W. / Hay, S. / Mulholland, A.J. / Leys, D. / Scrutton, N.S.
History
DepositionMay 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pentalenene synthase
B: Pentalenene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,15314
Polymers75,5492
Non-polymers1,60512
Water14,574809
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-21 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.810, 60.830, 64.100
Angle α, β, γ (deg.)90.04, 92.89, 101.98
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pentalenene synthase / 1 / 8-cineole synthase


Mass: 37774.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_p0982, SSCG_00536 / Production host: Escherichia coli (E. coli) / References: UniProt: B5GMG2, pentalenene synthase

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Non-polymers , 6 types, 821 molecules

#2: Chemical ChemComp-LA6 / (2E)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate


Mass: 332.200 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H19FO7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-9D2 / 2-ethyl-2-(hydroxymethyl)propane-1,3-diol


Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O3
#5: Chemical ChemComp-NDS / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE


Mass: 195.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3S
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 90mM of LiNaK (0.3M lithium sulphate, 0.3M sodium sulphate, 0.3 M potassium sulphate), 0.1M of buffer system 4 (1M MOPSO, 1M Bis-Tris) pH 6.5 and 50% precipitant mix 8 (10% PEG 20000, 50% ...Details: 90mM of LiNaK (0.3M lithium sulphate, 0.3M sodium sulphate, 0.3 M potassium sulphate), 0.1M of buffer system 4 (1M MOPSO, 1M Bis-Tris) pH 6.5 and 50% precipitant mix 8 (10% PEG 20000, 50% trimethyl propane, 2% NDSB 195)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.63→32.27 Å / Num. obs: 107492 / % possible obs: 96 % / Redundancy: 1.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.09 / Net I/σ(I): 6.7
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5258 / CC1/2: 0.479 / Rpim(I) all: 0.639 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2621: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1


Resolution: 1.63→32.264 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.37
RfactorNum. reflection% reflection
Rfree0.1938 5155 4.8 %
Rwork0.1662 --
obs0.1675 107482 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.63→32.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4943 0 98 809 5850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135283
X-RAY DIFFRACTIONf_angle_d1.157226
X-RAY DIFFRACTIONf_dihedral_angle_d10.253118
X-RAY DIFFRACTIONf_chiral_restr0.063755
X-RAY DIFFRACTIONf_plane_restr0.009947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.64850.31661380.29873388X-RAY DIFFRACTION95
1.6485-1.66790.25361460.29113349X-RAY DIFFRACTION94
1.6679-1.68830.3161780.27613403X-RAY DIFFRACTION94
1.6883-1.70960.30061690.27513299X-RAY DIFFRACTION95
1.7096-1.73210.29491660.26573461X-RAY DIFFRACTION95
1.7321-1.75590.28671520.25993345X-RAY DIFFRACTION95
1.7559-1.78090.2831420.253446X-RAY DIFFRACTION95
1.7809-1.80750.24841660.23353346X-RAY DIFFRACTION95
1.8075-1.83580.2421630.22853425X-RAY DIFFRACTION95
1.8358-1.86590.24361540.21993326X-RAY DIFFRACTION95
1.8659-1.8980.22281760.21453433X-RAY DIFFRACTION96
1.898-1.93250.20431770.19863386X-RAY DIFFRACTION96
1.9325-1.96970.21021810.20393416X-RAY DIFFRACTION96
1.9697-2.00990.25132010.17773387X-RAY DIFFRACTION95
2.0099-2.05360.20161700.16793388X-RAY DIFFRACTION96
2.0536-2.10140.19891680.16163444X-RAY DIFFRACTION96
2.1014-2.15390.18651430.16563424X-RAY DIFFRACTION96
2.1539-2.21210.21611800.15243440X-RAY DIFFRACTION97
2.2121-2.27720.17381900.14793380X-RAY DIFFRACTION97
2.2772-2.35070.17961640.13543452X-RAY DIFFRACTION97
2.3507-2.43470.1651740.12993468X-RAY DIFFRACTION97
2.4347-2.53210.14951680.1353482X-RAY DIFFRACTION97
2.5321-2.64730.17341710.13893429X-RAY DIFFRACTION97
2.6473-2.78680.18111730.14463455X-RAY DIFFRACTION98
2.7868-2.96130.17311880.13963442X-RAY DIFFRACTION97
2.9613-3.18970.17022010.14793456X-RAY DIFFRACTION97
3.1897-3.51040.17321860.13833403X-RAY DIFFRACTION97
3.5104-4.01750.16111950.12133449X-RAY DIFFRACTION97
4.0175-5.05850.13811890.13633420X-RAY DIFFRACTION97
5.0585-32.27030.24511860.20053385X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.06460.05040.01960.6914-0.16390.822-0.002-0.13820.02550.09340.01270.0353-0.0627-0.0553-0.0160.1088-0.0133-0.00970.106-0.00720.09697.855216.143525.3083
20.81130.02040.11721.1332-0.07340.71640.01570.1349-0.0311-0.1849-0.022-0.07460.04680.0744-0.00020.1256-0.00750.01050.11440.00620.099229.8148-1.67990.5473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 406)
2X-RAY DIFFRACTION2(chain 'B' and resid 4 through 406)

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