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- PDB-4lzc: W325F Epi-isozizaene synthase: Complex with Mg, inorganic pyropho... -

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Basic information

Entry
Database: PDB / ID: 4lzc
TitleW325F Epi-isozizaene synthase: Complex with Mg, inorganic pyrophosphate
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
PYROPHOSPHATE 2- / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.457 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 31, 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 / 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.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.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: Epi-isozizaene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0226
Polymers43,6771
Non-polymers3455
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.183, 47.070, 75.585
Angle α, β, γ (deg.)90.00, 95.79, 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: 43676.973 Da / Num. of mol.: 1 / Mutation: W325F
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-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-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: a 4 uL drop of protein solution [8 mg/mL W325F EIZS, 20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM MgCl2, 10% glycerol, 1 mM TCEP, 2 mM sodium pyrophosphate, 2 mM benzyltriethylammonium ...Details: a 4 uL drop of protein solution [8 mg/mL W325F EIZS, 20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM MgCl2, 10% glycerol, 1 mM TCEP, 2 mM sodium pyrophosphate, 2 mM benzyltriethylammonium chloride (BTAC)] was added to a 4 uL drop of precipitant solution [100 mM Bis-Tris (pH 5.5), 25-28% polyethylene glycol 3350, 0.2 M (NH4)2SO4] and equilibrated against a 1 mL reservoir of precipitant solution at 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2010 / Details: Kirpatrick Baez focusing mirrors
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.457→50 Å / Num. obs: 13755 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.148 / Rsym value: 0.148 / Net I/σ(I): 7.551
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.021 / Rsym value: 0.427 / % possible all: 99.9

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Processing

Software
NameVersionClassification
APS-24IDCIn House Programdata collection
PHASESphasing
PHENIX(phenix.refine: dev_1391)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID: 3KB9

3kb9


Resolution: 2.457→45.487 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 1374 10 %random
Rwork0.1819 ---
all0.1819 13755 --
obs0.1869 13741 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.457→45.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 17 47 2834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022866
X-RAY DIFFRACTIONf_angle_d0.5753906
X-RAY DIFFRACTIONf_dihedral_angle_d11.6141026
X-RAY DIFFRACTIONf_chiral_restr0.043406
X-RAY DIFFRACTIONf_plane_restr0.002507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.457-2.54480.28231330.21551190X-RAY DIFFRACTION97
2.5448-2.64670.27671350.2041222X-RAY DIFFRACTION100
2.6467-2.76710.26551380.20391254X-RAY DIFFRACTION100
2.7671-2.9130.31731340.19931204X-RAY DIFFRACTION100
2.913-3.09540.27281370.21111239X-RAY DIFFRACTION100
3.0954-3.33440.2641380.21511235X-RAY DIFFRACTION100
3.3344-3.66980.23621370.1721226X-RAY DIFFRACTION100
3.6698-4.20050.1991400.16151260X-RAY DIFFRACTION100
4.2005-5.29090.19341380.1521249X-RAY DIFFRACTION100
5.2909-45.49480.18431440.1721288X-RAY DIFFRACTION99

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