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- PDB-4ltv: Crystal structure of epi-isozizaene synthase from Streptomyces co... -

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Basic information

Entry
Database: PDB / ID: 4ltv
TitleCrystal structure of epi-isozizaene synthase from Streptomyces coelicolor A3(2)
ComponentsEpi-isozizaene synthase
KeywordsLYASE / Class I terpene cyclase
Function / homology
Function and homology information


epi-isozizaene synthase / epi-isozizaene synthase activity / 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
Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsLi, R. / Chou, W. / Himmelberger, J.A. / Litwin, K. / Harris, G. / Cane, D.E. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2014
Title: Reprogramming the Chemodiversity of Terpenoid Cyclization by Remolding the Active Site Contour of epi-Isozizaene Synthase.
Authors: Li, R. / Chou, W.K. / Himmelberger, J.A. / Litwin, K.M. / Harris, G.G. / Cane, D.E. / Christianson, D.W.
History
DepositionJul 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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 / _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: Epi-isozizaene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9083
Polymers43,7161
Non-polymers1922
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.238, 46.826, 75.817
Angle α, β, γ (deg.)90.00, 95.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Epi-isozizaene synthase / EIZS / Sesquiterpene cyclase / Sesquiterpene synthase


Mass: 43716.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: cyc1, SCO5222, SC7E4.19 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K499, epi-isozizaene synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 4 uL drop of protein solution [8-10 mg/mL EIZS, 20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM MgCl2, 10% glycerol, 2 mM TCEP, 2 mM sodium pyrophosphate, and 2 mM benzyltriethylammonium ...Details: 4 uL drop of protein solution [8-10 mg/mL EIZS, 20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM MgCl2, 10% glycerol, 2 mM TCEP, 2 mM sodium pyrophosphate, and 2 mM benzyltriethylammonium chloride] was added to 4 uL of precipitant solution [100 mM Bis-Tris (pH 5.5), 25-28%polyethylene glycol 3350, and 0.2M(NH4)2SO4] and equilibrated against a 1 mL well reservoir of precipitant solution. Crystals appeared within 2-3 days. Then the crystals were soaked in a chelation buffer [5 mM 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid, 15 mM ethylenediaminetetraacetic acid, 100 mM Bis-Tris (pH 5.5), 30% polyethylene glycol 3350, 200 mM (NH4)2SO4, 15% glycerol] for 7 days. , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Jan 31, 2012
Details: Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: ...Details: Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
RadiationMonochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13825 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 11.912
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.423 / Rsym value: 0.335 / % possible all: 94.5

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID: 3KB9

3kb9


Resolution: 2.403→41.068 Å / SU ML: 0.32 / σ(F): 0.07 / Phase error: 26.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1295 10.01 %
Rwork0.1911 --
obs0.197 12942 89.45 %
all-13825 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.233 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-19.5272 Å2-0 Å21.4346 Å2
2---8.6293 Å20 Å2
3----10.8978 Å2
Refinement stepCycle: LAST / Resolution: 2.403→41.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 10 53 2640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042663
X-RAY DIFFRACTIONf_angle_d0.7543626
X-RAY DIFFRACTIONf_dihedral_angle_d16.664938
X-RAY DIFFRACTIONf_chiral_restr0.051379
X-RAY DIFFRACTIONf_plane_restr0.003468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4034-2.49960.26191270.21791144X-RAY DIFFRACTION80
2.4996-2.61340.28981340.21651224X-RAY DIFFRACTION84
2.6134-2.75110.30931350.22831236X-RAY DIFFRACTION86
2.7511-2.92340.30651460.22441293X-RAY DIFFRACTION90
2.9234-3.14910.31231450.20091285X-RAY DIFFRACTION91
3.1491-3.46580.24711540.19651371X-RAY DIFFRACTION95
3.4658-3.9670.24451530.17951371X-RAY DIFFRACTION94
3.967-4.99660.22271480.16681357X-RAY DIFFRACTION93
4.9966-41.07450.20941530.18131366X-RAY DIFFRACTION91

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