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- PDB-3kb9: Epi-isozizaene synthase: Complex with Mg, inorganic pyrophosphate... -

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Basic information

Entry
Database: PDB / ID: 3kb9
TitleEpi-isozizaene synthase: Complex with Mg, inorganic pyrophosphate and benzyl triethyl ammonium cation
ComponentsEpi-isozizaene synthase
KeywordsLYASE / terpenoid cyclase / alpha-helical fold / farnesyl diphosphate / metal-binding / Magnesium
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
N-benzyl-N,N-diethylethanaminium / PYROPHOSPHATE 2- / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsAaron, J.A. / Lin, X. / Cane, D.E. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2010
Title: Structure of Epi-Isozizaene Synthase from Streptomyces coelicolor A3(2), a Platform for New Terpenoid Cyclization Templates
Authors: Aaron, J.A. / Lin, X. / Cane, D.E. / Christianson, D.W.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_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.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.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.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

Downloads & links

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Assembly

Deposited unit
A: Epi-isozizaene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62211
Polymers43,7161
Non-polymers90610
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.185, 47.374, 75.376
Angle α, β, γ (deg.)90.00, 95.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 43716.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: cyc1, SCO5222, SC7E4.19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K499, epi-isozizaene synthase

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Non-polymers , 6 types, 441 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Chemical ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 89364 / Num. obs: 46113 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rsym value: 0.058 / Net I/σ(I): 34.4
Reflection shellHighest resolution: 1.6 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 8.3 / Num. unique all: 4923 / Rsym value: 0.208 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.598→26.575 Å / SU ML: 0.19 / σ(F): 0.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1892 2232 4.96 %RANDOM
Rwork0.1579 ---
obs0.1595 45009 90.48 %-
all-46113 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.296 Å2 / ksol: 0.362 e/Å3
Refinement stepCycle: LAST / Resolution: 1.598→26.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 55 431 3344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123003
X-RAY DIFFRACTIONf_angle_d1.3984105
X-RAY DIFFRACTIONf_dihedral_angle_d20.9431115
X-RAY DIFFRACTIONf_chiral_restr0.091424
X-RAY DIFFRACTIONf_plane_restr0.008531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5979-1.63260.16941260.14572703X-RAY DIFFRACTION91
1.6326-1.67060.19391490.15252772X-RAY DIFFRACTION95
1.6706-1.71240.17121340.14292860X-RAY DIFFRACTION96
1.7124-1.75870.18251300.14832823X-RAY DIFFRACTION96
1.7587-1.81040.2161550.15482817X-RAY DIFFRACTION97
1.8104-1.86880.19261470.15992844X-RAY DIFFRACTION97
1.8688-1.93560.22151440.16342502X-RAY DIFFRACTION85
1.9356-2.01310.19771670.1682812X-RAY DIFFRACTION97
2.0131-2.10470.17581770.15142896X-RAY DIFFRACTION99
2.1047-2.21560.18031380.15262654X-RAY DIFFRACTION96
2.2156-2.35430.2013970.1521744X-RAY DIFFRACTION69
2.3543-2.5360.19971400.15682967X-RAY DIFFRACTION99
2.536-2.79090.16851610.15532944X-RAY DIFFRACTION99
2.7909-3.19420.19141670.15812919X-RAY DIFFRACTION99
3.1942-4.02210.1874740.14781487X-RAY DIFFRACTION49
4.0221-26.57840.16721260.15043033X-RAY DIFFRACTION98

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