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- PDB-4lxw: L72V Epi-isozizaene synthase: Complex with Mg, inorganic pyrophos... -

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Basic information

Entry
Database: PDB / ID: 4lxw
TitleL72V Epi-isozizaene synthase: Complex with Mg, inorganic pyrophosphate and benzyl triethyl ammonium cation
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
N-benzyl-N,N-diethylethanaminium / PYROPHOSPHATE 2- / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 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 30, 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)44,4239
Polymers43,7021
Non-polymers7218
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.977, 47.236, 75.084
Angle α, β, γ (deg.)90.00, 95.66, 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: 43701.984 Da / Num. of mol.: 1 / Mutation: L72V
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

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Non-polymers , 6 types, 249 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: A 4 uL drop of protein solution [8 mg/mL L72V 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 L72V 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 room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2010
Details: Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at3.3:1 demagnification. Mirror: ...Details: Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at3.3:1 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: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.092→50 Å / Num. obs: 22011 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 12.204
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 3.479 / Rsym value: 0.301 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID: 3KB9

3kb9


Resolution: 2.092→41.203 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 2000 9.09 %
Rwork0.1727 --
obs0.1758 21998 99.5 %
all-22011 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.4288 Å2-0 Å22.907 Å2
2---0.3348 Å20 Å2
3----5.094 Å2
Refinement stepCycle: LAST / Resolution: 2.092→41.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 43 241 3064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022912
X-RAY DIFFRACTIONf_angle_d0.6493969
X-RAY DIFFRACTIONf_dihedral_angle_d13.3531046
X-RAY DIFFRACTIONf_chiral_restr0.048410
X-RAY DIFFRACTIONf_plane_restr0.002513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0921-2.14440.27321360.2141354X-RAY DIFFRACTION94
2.1444-2.20240.24581400.20521400X-RAY DIFFRACTION99
2.2024-2.26720.21471420.18011423X-RAY DIFFRACTION100
2.2672-2.34030.27051430.18781433X-RAY DIFFRACTION100
2.3403-2.4240.24511430.18231423X-RAY DIFFRACTION100
2.424-2.5210.22621430.17751433X-RAY DIFFRACTION100
2.521-2.63570.21061420.1781419X-RAY DIFFRACTION100
2.6357-2.77460.2331420.19691425X-RAY DIFFRACTION100
2.7746-2.94840.23721440.19351442X-RAY DIFFRACTION100
2.9484-3.1760.2471420.20071414X-RAY DIFFRACTION100
3.176-3.49550.21391430.18071436X-RAY DIFFRACTION100
3.4955-4.00090.17591450.15071458X-RAY DIFFRACTION100
4.0009-5.03930.1481460.13051444X-RAY DIFFRACTION100
5.0393-41.21130.14051490.14841494X-RAY DIFFRACTION100

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