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- PDB-1n21: (+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3-aza-2,3-... -

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Basic information

Entry
Database: PDB / ID: 1n21
Title(+)-Bornyl Diphosphate Synthase: Cocrystal with Mg and 3-aza-2,3-dihydrogeranyl diphosphate
Components(+)-bornyl diphosphate synthase
KeywordsISOMERASE / terpene synthase fold
Function / homology
Function and homology information


(+)-camphene synthase / (+)-alpha-pinene synthase / (+)-bornyl diphosphate synthase / (+)-camphor biosynthetic process / geranyl-diphosphate cyclase activity / camphene synthase activity / 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
Chem-3AG / (+)-bornyl diphosphate synthase, chloroplastic
Similarity search - Component
Biological speciesSalvia officinalis (garden sage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 synthase
Authors: Whittington, D.A. / Wise, M.L. / Urbansky, M. / Coates, R.M. / Croteau, R.B. / Christianson, D.W.
History
DepositionOct 21, 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 1.3Feb 14, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,4235
Polymers64,0361
Non-polymers3874
Water46826
1
A: (+)-bornyl diphosphate synthase
hetero molecules

A: (+)-bornyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,84610
Polymers128,0712
Non-polymers7748
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)198.38, 198.38, 122.84
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a dimer, consisting of the molecule in the asymmetric unit and the molecule generated by the operation: -y, -x, -z+1/2

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Components

#1: Protein (+)-bornyl diphosphate synthase


Mass: 64035.664 Da / Num. of mol.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-3AG / 2-[METHYL-(4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE / 3-AZA-2,3-DIHYDROGERANYL DIPHOSPHATE


Mass: 314.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H18NO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 5.6 Å3/Da / Density % sol: 77.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG 8000, glycerol, bis-tris, magnesium chloride, dithiothreitol, 2-aza-2,3-dihydrogeranyl diphosphate , 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: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 26476 / Num. obs: 26476 / % possible obs: 100 % / Redundancy: 33 % / Rsym value: 0.087 / Net I/σ(I): 33
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 13.6 / Num. unique all: 2585 / Rsym value: 0.215 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 30 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N1B

1n1b


Resolution: 3.1→29.93 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME, BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2072 7.9 %RANDOM
Rwork0.207 ---
obs0.207 26300 100 %-
all-26301 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 16.4271 Å2 / ksol: 0.281615 e/Å3
Displacement parametersBiso mean: 42.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å22.95 Å20 Å2
2--1.72 Å20 Å2
3----3.43 Å2
Refine analyzeLuzzati coordinate error free: 0.39 Å / Luzzati sigma a free: 0.52 Å
Refinement stepCycle: LAST / Resolution: 3.1→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 22 26 4453
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it7.451.5
X-RAY DIFFRACTIONc_mcangle_it11.582
X-RAY DIFFRACTIONc_scbond_it11.092
X-RAY DIFFRACTIONc_scangle_it16.252.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 311 7.3 %
Rwork0.253 3964 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4AGP.PARAMAGP.TOP
Refinement
*PLUS
Highest resolution: 3.1 Å / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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