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- PDB-2j5c: Rational conversion of substrate and product specificity in a mon... -

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Basic information

Entry
Database: PDB / ID: 2j5c
TitleRational conversion of substrate and product specificity in a monoterpene synthase. Structural insights into the molecular basis of rapid evolution.
Components1,8-CINEOLE SYNTHASE
KeywordsLYASE / TERPENE SYNTHASES / 1 / 8-CINEOLE / MONOTERPENE
Function / homology
Function and homology information


terpene synthase activity / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Terpene cyclase-like 1, C-terminal domain / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Cineole synthase
Similarity search - Component
Biological speciesSALVIA FRUTICOSA (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKampranis, S.C. / Ioannidis, D. / Purvis, A. / Mahrez, W. / Ninga, E. / Katerelos, N.A. / Anssour, S. / Dunwell, J.M. / Makris, A.M. / Goodenough, P.W. / Johnson, C.B.
CitationJournal: Plant Cell / Year: 2007
Title: Rational Conversion of Substrate and Product Specificity in a Salvia Monoterpene Synthase: Structural Insights Into the Evolution of Terpene Synthase Function.
Authors: Kampranis, S.C. / Ioannidis, D. / Purvis, A. / Mahrez, W. / Ninga, E. / Katerelos, N.A. / Anssour, S. / Dunwell, J.M. / Degenhardt, J. / Makris, A.M. / Goodenough, P.W. / Johnson, C.B.
History
DepositionSep 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,8-CINEOLE SYNTHASE
B: 1,8-CINEOLE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,8416
Polymers134,5292
Non-polymers3134
Water8,269459
1
A: 1,8-CINEOLE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4213
Polymers67,2641
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 1,8-CINEOLE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4213
Polymers67,2641
Non-polymers1562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.550, 171.150, 123.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2141-

HOH

21B-2157-

HOH

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Components

#1: Protein 1,8-CINEOLE SYNTHASE /


Mass: 67264.312 Da / Num. of mol.: 2 / Fragment: RESIDUES 58-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALVIA FRUTICOSA (plant) / Strain: M. SKOULA 824 (TUCCG)
Description: WILD SOURCE FOUND IN NIO CHORIO, CHANIA, CRETE, GREECE
Plasmid: PRSET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: A6XH05*PLUS, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O
Sequence details1,8-CINEOLE SYNTHASE SEQUENCE STARTS AT ARG58 WHICH IS PRECEDED BY A 35 RESIDUE N-TERMINAL LEADING ...1,8-CINEOLE SYNTHASE SEQUENCE STARTS AT ARG58 WHICH IS PRECEDED BY A 35 RESIDUE N-TERMINAL LEADING SEQUENCE WHICH CONTAINS A HIS-TAG

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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: 2.46 Å3/Da / Density % sol: 49.9 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP METHOD OF VAPOUR DIFFUSION USING 100MM TRIS PH 8.0, 5MM BETA-MERCAPTOETHANOL, 1.0M SODIUM FORMATE, 10% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2005 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 354544 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N1B

1n1b


Resolution: 1.95→29.7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2844174.15 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CIS-PEPTIDE PRESENT IN BOTH MOLECULES AT TYROSINE 474. DISORDERED REGIONS IN MOLECULE A (N -TERMINUS-83, 224-227, 306-307, 494-503, 511-516, 573) AND MOLECULE B (N-TERMINUS-86, 226-227, 493- ...Details: CIS-PEPTIDE PRESENT IN BOTH MOLECULES AT TYROSINE 474. DISORDERED REGIONS IN MOLECULE A (N -TERMINUS-83, 224-227, 306-307, 494-503, 511-516, 573) AND MOLECULE B (N-TERMINUS-86, 226-227, 493-502, 572-573) WERE OMITTED FROM THE STRUCTURE. DISORDERED SIDE CHAINS OF UNDETERMINED ORIENTATION WERE REMOVED FROM THE STRUCTURE (127 ATOMS IN TOTAL).
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4786 5 %RANDOM
Rwork0.218 ---
obs0.218 95726 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2915 Å2 / ksol: 0.348814 e/Å3
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-11.01 Å20 Å20 Å2
2---1.76 Å20 Å2
3----9.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.95→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7993 0 16 459 8468
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.026
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.792.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 775 4.9 %
Rwork0.269 14907 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PRODRG_BME_MODIFIED.PARPRODRG_BME_MODIFIED.TOP

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