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- PDB-4lz3: F95H Epi-isozizaene synthase: Complex with Mg, inorganic pyrophos... -

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Basic information

Entry
Database: PDB / ID: 4lz3
TitleF95H 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 / 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 / HYDROGENPHOSPHATE ION / PYROPHOSPHATE 2- / Epi-isozizaene synthase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 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)44,61311
Polymers43,7071
Non-polymers90610
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.707, 75.644, 107.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 43706.984 Da / Num. of mol.: 1 / Mutation: F95H
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, 278 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 192.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N
#6: Chemical ChemComp-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO4P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAt pH 7.5, theoretically, both dihydrogen phosphate and hydrogen phosphate ions are present with a ...At pH 7.5, theoretically, both dihydrogen phosphate and hydrogen phosphate ions are present with a ratio around 1:2. In the crystal structure of F95H EIZS, the dihydrogen phosphate /hydrogen phosphate ion is surrounded and stabilized by three Arginine side chains, one Histidine side chain, one glycerol and two water molecules. The contacts involving hydrogen bonding interaction and salt bridge interaction between each oxygen of dihydrogen phosphate /hydrogen phosphate ion and surrounding molecules indicates that hydrogen phosphate ion would be a reasonable fit in such electropositive environment.

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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: 43.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: A 0.6 uL drop of protein solution [10 mg/mL F95H EIZS, 20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM MgCl2, 10% glycerol, 2 mM TCEP, 2 mM sodium pyrophosphate, 2 mM BTAC] was added to 0.6 uL ...Details: A 0.6 uL drop of protein solution [10 mg/mL F95H EIZS, 20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 10 mM MgCl2, 10% glycerol, 2 mM TCEP, 2 mM sodium pyrophosphate, 2 mM BTAC] was added to 0.6 uL of precipitant solution [40 mM KH2PO4, 16% polyethylene glycol 8000, and 20% glycerol] and equilibrated against a 110 uL well reservoir of precipitant solution., VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2013
Details: Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: ...Details: Monochromator: Double silicon (111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 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: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.095→50 Å / Num. obs: 23067 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 11.859
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.917 / Rsym value: 0.323 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata 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: 2.095→43.829 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 18.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 2000 8.69 %random
Rwork0.1603 ---
all0.1603 23067 --
obs0.1642 23015 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.095→43.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 55 268 3103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032929
X-RAY DIFFRACTIONf_angle_d0.7453992
X-RAY DIFFRACTIONf_dihedral_angle_d14.2291051
X-RAY DIFFRACTIONf_chiral_restr0.054414
X-RAY DIFFRACTIONf_plane_restr0.003514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0948-2.14720.23561330.15871391X-RAY DIFFRACTION94
2.1472-2.20530.21531390.15351468X-RAY DIFFRACTION100
2.2053-2.27020.2061420.15421491X-RAY DIFFRACTION100
2.2702-2.34340.22961420.15491497X-RAY DIFFRACTION100
2.3434-2.42720.21691400.15711466X-RAY DIFFRACTION100
2.4272-2.52440.20561420.15561489X-RAY DIFFRACTION100
2.5244-2.63920.18051410.1541487X-RAY DIFFRACTION100
2.6392-2.77840.21081440.16341505X-RAY DIFFRACTION100
2.7784-2.95240.24171410.16311496X-RAY DIFFRACTION100
2.9524-3.18030.20081440.16641508X-RAY DIFFRACTION100
3.1803-3.50020.21391430.16141499X-RAY DIFFRACTION100
3.5002-4.00640.19161470.15291535X-RAY DIFFRACTION100
4.0064-5.04650.16451470.14721551X-RAY DIFFRACTION100
5.0465-43.83830.21461550.18941632X-RAY DIFFRACTION100

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