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- PDB-4luu: V329A Epi-isozizaene synthase: Complex with Mg, inorganic pyropho... -

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Basic information

Entry
Database: PDB / ID: 4luu
TitleV329A 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: 1.95 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 25, 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)44,4139
Polymers43,6881
Non-polymers7258
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.214, 47.485, 75.283
Angle α, β, γ (deg.)90.00, 95.50, 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: 43687.961 Da / Num. of mol.: 1 / Mutation: V329A
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, 384 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.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: a 4 uL drop of protein solution [8 mg/mL V329A 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 V329A 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: 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: 1.95→50 Å / Num. obs: 26839 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 12.957
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.029 / Rsym value: 0.432 / % possible all: 97.4

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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: 1.95→32.797 Å / SU ML: 0.19 / σ(F): 0.13 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 2027 7.97 %random
Rwork0.1516 ---
all0.1516 26839 --
obs0.1557 25420 92.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.373 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7947 Å20 Å24.0322 Å2
2--4.4751 Å20 Å2
3----6.2698 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 42 376 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072937
X-RAY DIFFRACTIONf_angle_d1.0144007
X-RAY DIFFRACTIONf_dihedral_angle_d16.6271065
X-RAY DIFFRACTIONf_chiral_restr0.064411
X-RAY DIFFRACTIONf_plane_restr0.005519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9496-1.99840.25941390.17861494X-RAY DIFFRACTION84
1.9984-2.05240.25051340.17591623X-RAY DIFFRACTION89
2.0524-2.11280.26061500.15651612X-RAY DIFFRACTION91
2.1128-2.1810.22451560.16631650X-RAY DIFFRACTION92
2.181-2.25890.2591200.17131607X-RAY DIFFRACTION89
2.2589-2.34930.1981330.1471554X-RAY DIFFRACTION86
2.3493-2.45620.21731440.1371725X-RAY DIFFRACTION96
2.4562-2.58570.19011480.14171756X-RAY DIFFRACTION97
2.5857-2.74760.18411400.14851783X-RAY DIFFRACTION98
2.7476-2.95960.18871520.15341803X-RAY DIFFRACTION98
2.9596-3.25720.2041620.1561769X-RAY DIFFRACTION99
3.2572-3.7280.18281380.14741433X-RAY DIFFRACTION79
3.728-4.69460.15811550.13111700X-RAY DIFFRACTION93
4.6946-32.80130.18811560.15011884X-RAY DIFFRACTION99

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