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- PDB-1n1b: Crystal Structure of (+)-Bornyl Diphosphate Synthase from Sage -

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Basic information

Entry
Database: PDB / ID: 1n1b
TitleCrystal Structure of (+)-Bornyl Diphosphate Synthase from Sage
Components(+)-bornyl diphosphate synthase
KeywordsISOMERASE / terpene synthase fold
Function / homology
Function and homology information


(+)-camphene synthase / (+)-bornyl diphosphate synthase / (+)-camphor biosynthetic process / geranyl-diphosphate cyclase activity / camphene synthase activity / (+)-alpha-pinene synthase / pinene synthase activity / diterpenoid biosynthetic process / chloroplast / magnesium ion binding / protein homodimerization activity
Similarity search - Function
Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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 ...Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / 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
: / (+)-bornyl diphosphate synthase, chloroplastic
Similarity search - Component
Biological speciesSalvia officinalis (garden sage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsWhittington, D.A. / Wise, M.L. / Urbansky, M. / Coates, R.M. / Croteau, R.B. / Christianson, D.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Bornyl Diphosphate Synthase: Structure and Strategy for Carbocation Manipulation by a Terpenoid Cyclase
Authors: Whittington, D.A. / Wise, M.L. / Urbansky, M. / Coates, R.M. / Croteau, R.B. / Christianson, D.W.
History
DepositionOct 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (+)-bornyl diphosphate synthase
B: (+)-bornyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,32615
Polymers128,0712
Non-polymers2,25513
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-317 kcal/mol
Surface area44120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.06, 116.77, 120.34
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the dimer contained in the asymmetric unit.

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Components

#1: Protein (+)-bornyl diphosphate synthase


Mass: 64035.664 Da / Num. of mol.: 2 / Fragment: residue 50-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salvia officinalis (garden sage) / Plasmid: pSBET / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3)
References: UniProt: O81192, (+)-bornyl diphosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.8 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 8000, glycerol, bis-Tris, magnesium chloride, potassium mercury thiocyanate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlenzyme1drop
21 mMdithiothreitol1drop
320 mMBis-Tris1droppH6.8
410 %(w/v)PEG80001reservoir
515 %(v/v)glycerol1reservoir
62 mMdithiothreitol1reservoiror 1mM potassium mercury thiocyanate
7220 mM1reservoirMgCl2
80.1 MBis-Tris1reservoirpH6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 97291 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 33.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4 / Num. unique all: 4640 / Rsym value: 0.442 / % possible all: 97.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 633848 / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.83 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3756 4 %RANDOM
Rwork0.203 ---
obs0.203 93609 95.9 %-
all-97450 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.1991 Å2 / ksol: 0.359857 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.43 Å20 Å20 Å2
2---3.34 Å20 Å2
3----1.09 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8555 0 13 588 9156
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.811.5
X-RAY DIFFRACTIONc_mcangle_it2.572
X-RAY DIFFRACTIONc_scbond_it2.762
X-RAY DIFFRACTIONc_scangle_it3.952.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 569 3.9 %
Rwork0.235 14032 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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