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- PDB-4la5: Crystal structure of 2-methylisoborneol synthase from Streptomyce... -

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Basic information

Entry
Database: PDB / ID: 4la5
TitleCrystal structure of 2-methylisoborneol synthase from Streptomyces coelicolor A3(2)
Components2-methylisoborneol synthase
KeywordsLYASE / terpenoid biosynthesis / biosynthesis / isoprenoid synthase fold
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
2-methylisoborneol synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsKoksal, M. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2013
Title: Unexpected reactivity of 2-fluorolinalyl diphosphate in the active site of crystalline 2-methylisoborneol synthase.
Authors: Koksal, M. / Chou, W.K. / Cane, D.E. / Christianson, D.W.
History
DepositionJun 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-methylisoborneol synthase


Theoretical massNumber of molelcules
Total (without water)50,1451
Polymers50,1451
Non-polymers00
Water2,612145
1
A: 2-methylisoborneol synthase

A: 2-methylisoborneol synthase


Theoretical massNumber of molelcules
Total (without water)100,2902
Polymers100,2902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area5090 Å2
ΔGint-36 kcal/mol
Surface area24410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.451, 99.451, 104.891
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, 2-methylisoborneol synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 52.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM bis-Tris (pH 6.5), 25% polyethylene glycol 3350, 200 mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 45521 / Num. obs: 45481 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 30.25 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 35.714
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 11 % / Rmerge(I) obs: 0.01168 / Mean I/σ(I) obs: 2.11 / Num. unique all: 4408 / Rsym value: 0.01168 / % possible all: 99.1

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Processing

Software
NameClassification
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V1V

3v1v


Resolution: 1.849→49.725 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 1855 4.34 %random
Rwork0.1859 ---
all0.1872 45521 --
obs0.1872 42739 93.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.425 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.5272 Å2-0 Å20 Å2
2---3.5272 Å2-0 Å2
3---7.0544 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.849→49.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 0 145 2671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0352611
X-RAY DIFFRACTIONf_angle_d2.4023570
X-RAY DIFFRACTIONf_dihedral_angle_d17.9924
X-RAY DIFFRACTIONf_chiral_restr0.201377
X-RAY DIFFRACTIONf_plane_restr0.015475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8494-1.89940.35151160.26912602X-RAY DIFFRACTION79
1.8994-1.95530.2571210.24972770X-RAY DIFFRACTION84
1.9553-2.01840.27061290.22192883X-RAY DIFFRACTION88
2.0184-2.09050.25671380.21093023X-RAY DIFFRACTION92
2.0905-2.17420.271480.20813081X-RAY DIFFRACTION94
2.1742-2.27320.25541380.19843166X-RAY DIFFRACTION95
2.2732-2.3930.25631440.18733211X-RAY DIFFRACTION97
2.393-2.54290.22261540.18453221X-RAY DIFFRACTION97
2.5429-2.73930.22051410.18623276X-RAY DIFFRACTION98
2.7393-3.01490.20931490.18653323X-RAY DIFFRACTION98
3.0149-3.45110.19831550.18283338X-RAY DIFFRACTION99
3.4511-4.34760.17511560.16083400X-RAY DIFFRACTION99
4.3476-49.74350.18991660.17113590X-RAY DIFFRACTION99

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