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- PDB-6axn: F95C Epi-isozizaene synthase -

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Basic information

Entry
Database: PDB / ID: 6axn
TitleF95C Epi-isozizaene synthase
ComponentsEpi-isozizaene synthase
KeywordsLYASE / Terpenoid Cyclase
Function / homology
Function and homology information


epi-isozizaene synthase / epi-isozizaene 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: 1.9 Å
AuthorsBlank, P.N. / Barrow, G.H. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM56838 United States
CitationJournal: Biochemistry / Year: 2017
Title: Substitution of Aromatic Residues with Polar Residues in the Active Site Pocket of epi-Isozizaene Synthase Leads to the Generation of New Cyclic Sesquiterpenes.
Authors: Blank, P.N. / Barrow, G.H. / Chou, W.K.W. / Duan, L. / Cane, D.E. / Christianson, D.W.
History
DepositionSep 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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

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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)44,2097
Polymers43,6721
Non-polymers5376
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.614, 46.787, 75.371
Angle α, β, γ (deg.)90.00, 98.16, 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 cyclase / Sesquiterpene synthase


Mass: 43671.980 Da / Num. of mol.: 1 / Mutation: F95C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: ATCC BAA-471 / A3(2) / M145 / Gene: cyc1, SCO5222, SC7E4.19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K499, epi-isozizaene synthase

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Non-polymers , 5 types, 193 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-


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2.6H2O, 0.1 M bis-Tris (pH 6.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 1.9→32.53 Å / Num. obs: 28111 / % possible obs: 98.8 % / Redundancy: 4.1 % / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KB9

3kb9


Resolution: 1.9→32.53 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.1906 1406 5 %
Rwork0.1573 --
obs0.159 28104 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→32.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 31 187 2934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152828
X-RAY DIFFRACTIONf_angle_d1.4613865
X-RAY DIFFRACTIONf_dihedral_angle_d14.451005
X-RAY DIFFRACTIONf_chiral_restr0.072408
X-RAY DIFFRACTIONf_plane_restr0.008498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8977-1.96550.22571290.18882453X-RAY DIFFRACTION92
1.9655-2.04420.22881400.18352647X-RAY DIFFRACTION99
2.0442-2.13720.2261400.1672664X-RAY DIFFRACTION99
2.1372-2.24990.22031400.15322680X-RAY DIFFRACTION99
2.2499-2.39080.22761400.15182651X-RAY DIFFRACTION100
2.3908-2.57530.20291430.15242704X-RAY DIFFRACTION100
2.5753-2.83440.21181410.16012676X-RAY DIFFRACTION100
2.8344-3.24430.21420.15742716X-RAY DIFFRACTION100
3.2443-4.08640.15991430.14422720X-RAY DIFFRACTION100
4.0864-34.51080.16331480.162787X-RAY DIFFRACTION100

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