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- PDB-3v1x: Crystal structure of 2-methylisoborneol synthase from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 3v1x
TitleCrystal structure of 2-methylisoborneol synthase from Streptomyces coelicolor A3(2) in complex with Mg2+ and 2-fluorogeranyl diphosphate
Components2-methylisoborneol synthase
KeywordsLYASE / class I terpenoid cyclase fold / DDXXXXD motif / NDXXSXXXE motif / 2-methylisoborneol biosynthesis / Biosynthesis of 2-methylisoborneol
Function / homology
Function and homology information


2-methylisoborneol synthase / terpene metabolic process / terpene synthase activity / metal ion binding
Similarity search - Function
: / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0FV / 2-methylisoborneol synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.955 Å
AuthorsKoksal, M. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2012
Title: Structure of 2-Methylisoborneol Synthase from Streptomyces coelicolor and Implications for the Cyclization of a Noncanonical C-Methylated Monoterpenoid Substrate.
Authors: Koksal, M. / Chou, W.K. / Cane, D.E. / Christianson, D.W.
History
DepositionDec 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: 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_ref_seq_dif / 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.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_ref_seq_dif.details / _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: 2-methylisoborneol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5264
Polymers50,1451
Non-polymers3813
Water4,504250
1
A: 2-methylisoborneol synthase
hetero molecules

A: 2-methylisoborneol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0518
Polymers100,2902
Non-polymers7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/41
Buried area5130 Å2
ΔGint-37 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.635, 99.635, 104.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein 2-methylisoborneol synthase / 2-MIB synthase


Mass: 50144.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SC1A4.08, SCBAC12C8.01, SCO7700 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9F1Y6, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-0FV / (2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate / 2-fluorogeranyl diphosphate


Mass: 332.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H19FO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8 M Succinic acid pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 11, 2011
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 38813 / Num. obs: 37222 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 14.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3531 / Rsym value: 0.849 / % possible all: 93.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXAutoMRmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V1V

3v1v


Resolution: 1.955→46.381 Å / SU ML: 0.21 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 21.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 1881 5.38 %RANDOM
Rwork0.1764 ---
all0.1787 38813 --
obs0.1787 34994 90.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.325 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3536 Å2-0 Å20 Å2
2---3.3536 Å2-0 Å2
3---6.7073 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.021 Å0.021 Å
Luzzati d res low-5 Å
Luzzati sigma a0.021 Å0.019 Å
Refinement stepCycle: LAST / Resolution: 1.955→46.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 22 250 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222585
X-RAY DIFFRACTIONf_angle_d1.7883536
X-RAY DIFFRACTIONf_dihedral_angle_d17.94930
X-RAY DIFFRACTIONf_chiral_restr0.128371
X-RAY DIFFRACTIONf_plane_restr0.011469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9546-2.00750.29081300.23122189X-RAY DIFFRACTION80
2.0075-2.06660.27281310.21662306X-RAY DIFFRACTION83
2.0666-2.13330.23791250.19942315X-RAY DIFFRACTION84
2.1333-2.20950.24371430.17392394X-RAY DIFFRACTION86
2.2095-2.2980.20661350.18132504X-RAY DIFFRACTION89
2.298-2.40260.24771530.18122533X-RAY DIFFRACTION91
2.4026-2.52920.26091430.1932606X-RAY DIFFRACTION93
2.5292-2.68770.23851490.18692622X-RAY DIFFRACTION93
2.6877-2.89520.22211510.17912627X-RAY DIFFRACTION93
2.8952-3.18640.22211540.18252669X-RAY DIFFRACTION94
3.1864-3.64740.21351550.16862730X-RAY DIFFRACTION96
3.6474-4.59470.1821480.14412752X-RAY DIFFRACTION95
4.5947-46.39410.19061640.16982866X-RAY DIFFRACTION94

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