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- PDB-6w26: Terpenoid Cyclase FgGS in Complex with Mg, Inorganic Pyrophosphat... -

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Basic information

Entry
Database: PDB / ID: 6w26
TitleTerpenoid Cyclase FgGS in Complex with Mg, Inorganic Pyrophosphate, and Imidazole
ComponentsTerpenoid cyclase FgGS
KeywordsLYASE / terpene / terpenoid
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on phosphates / terpene synthase activity / isoprenoid biosynthetic process / 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
IMIDAZOLE / PYROPHOSPHATE 2- / Terpene synthase
Similarity search - Component
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHerbst-Gervasoni, C.J. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM56838 United States
CitationJournal: Nat Commun / Year: 2020
Title: Discovery of the cryptic function of terpene cyclases as aromatic prenyltransferases.
Authors: He, H. / Bian, G. / Herbst-Gervasoni, C.J. / Mori, T. / Shinsky, S.A. / Hou, A. / Mu, X. / Huang, M. / Cheng, S. / Deng, Z. / Christianson, D.W. / Abe, I. / Liu, T.
History
DepositionMar 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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_auth_asym_id / _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_asym_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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Terpenoid cyclase FgGS
A: Terpenoid cyclase FgGS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,59521
Polymers72,3782
Non-polymers1,21719
Water3,567198
1
I: Terpenoid cyclase FgGS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,91112
Polymers36,1891
Non-polymers72211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Terpenoid cyclase FgGS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6849
Polymers36,1891
Non-polymers4958
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 87.201, 163.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERARGARG(chain 'A' and (resid 5 through 14 or (resid 15...AB5 - 445 - 44
12ASPASPPROPRO(chain 'A' and (resid 5 through 14 or (resid 15...AB46 - 5346 - 53
13THRTHRASNASN(chain 'A' and (resid 5 through 14 or (resid 15...AB55 - 6155 - 61
14ILEILELEULEU(chain 'A' and (resid 5 through 14 or (resid 15...AB63 - 7463 - 74
15ARGARGGLUGLU(chain 'A' and (resid 5 through 14 or (resid 15...AB76 - 10076 - 100
16ALAALAILEILE(chain 'A' and (resid 5 through 14 or (resid 15...AB110 - 122110 - 122
17ARGARGVALVAL(chain 'A' and (resid 5 through 14 or (resid 15...AB124 - 131124 - 131
18ALAALALYSLYS(chain 'A' and (resid 5 through 14 or (resid 15...AB133 - 151133 - 151
19VALVALMETMET(chain 'A' and (resid 5 through 14 or (resid 15...AB153 - 166153 - 166
110ASPASPMETMET(chain 'A' and (resid 5 through 14 or (resid 15...AB168 - 184168 - 184
111LEULEUASPASP(chain 'A' and (resid 5 through 14 or (resid 15...AB186 - 215186 - 215
112GLUGLUVALVAL(chain 'A' and (resid 5 through 14 or (resid 15...AB217 - 221217 - 221
113THRTHRILEILE(chain 'A' and (resid 5 through 14 or (resid 15...AB223 - 263223 - 263
114GLUGLULYSLYS(chain 'A' and (resid 5 through 14 or (resid 15...AB265 - 270265 - 270
115PROPROPROPRO(chain 'A' and (resid 5 through 14 or (resid 15...AB272 - 303272 - 303
216SERSERARGARG(chain 'I' and (resid 5 through 40 or (resid 41...IA5 - 445 - 44
217ASPASPPROPRO(chain 'I' and (resid 5 through 40 or (resid 41...IA46 - 5346 - 53
218THRTHRASNASN(chain 'I' and (resid 5 through 40 or (resid 41...IA55 - 6155 - 61
219ILEILELEULEU(chain 'I' and (resid 5 through 40 or (resid 41...IA63 - 7463 - 74
220ARGARGGLUGLU(chain 'I' and (resid 5 through 40 or (resid 41...IA76 - 10076 - 100
221ALAALAILEILE(chain 'I' and (resid 5 through 40 or (resid 41...IA110 - 122110 - 122
222ARGARGVALVAL(chain 'I' and (resid 5 through 40 or (resid 41...IA124 - 131124 - 131
223ALAALALYSLYS(chain 'I' and (resid 5 through 40 or (resid 41...IA133 - 151133 - 151
224VALVALMETMET(chain 'I' and (resid 5 through 40 or (resid 41...IA153 - 166153 - 166
225ASPASPMETMET(chain 'I' and (resid 5 through 40 or (resid 41...IA168 - 184168 - 184
226LEULEUASPASP(chain 'I' and (resid 5 through 40 or (resid 41...IA186 - 215186 - 215
227GLUGLUVALVAL(chain 'I' and (resid 5 through 40 or (resid 41...IA217 - 221217 - 221
228THRTHRILEILE(chain 'I' and (resid 5 through 40 or (resid 41...IA223 - 263223 - 263
229GLUGLULYSLYS(chain 'I' and (resid 5 through 40 or (resid 41...IA265 - 270265 - 270
230PROPROPROPRO(chain 'I' and (resid 5 through 40 or (resid 41...IA272 - 303272 - 303

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Components

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Protein , 1 types, 2 molecules IA

#1: Protein Terpenoid cyclase FgGS


Mass: 36188.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella zeae (strain PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084) (fungus)
Strain: PH-1 / ATCC MYA-4620 / FGSC 9075 / NRRL 31084 / Gene: FGRAMPH1_01T04331 / Production host: Escherichia coli (E. coli) / References: UniProt: I1RDR8

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Non-polymers , 8 types, 217 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5 mg/mL FgGS, 2 mM indole, 10 mM magnesium chloride, 2 mM sodium pyrophosphate, 0.1 M Ammonium sulfate, 0.1 M Imidazole (pH 7.3), 24% (w/v) PEG monomethyl ether 5k, and 2% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.15→46.82 Å / Num. obs: 38801 / % possible obs: 99.52 % / Redundancy: 6 % / Biso Wilson estimate: 19.84 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.09022 / Rpim(I) all: 0.09022 / Net I/σ(I): 4.9
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.2517 / Mean I/σ(I) obs: 2.83 / Num. unique obs: 3834 / CC1/2: 0.642 / Rpim(I) all: 0.2517

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TD7

5td7


Resolution: 2.15→46.82 Å / SU ML: 0.2805 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2009 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2544 1949 5.03 %
Rwork0.2036 36829 -
obs0.2062 38778 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.41 Å2
Refinement stepCycle: LAST / Resolution: 2.15→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4717 0 70 198 4985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614938
X-RAY DIFFRACTIONf_angle_d0.66116700
X-RAY DIFFRACTIONf_chiral_restr0.0445750
X-RAY DIFFRACTIONf_plane_restr0.0038861
X-RAY DIFFRACTIONf_dihedral_angle_d22.74561825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.31521310.25772579X-RAY DIFFRACTION99.78
2.2-2.260.3461350.27172567X-RAY DIFFRACTION98.61
2.26-2.330.30591140.24742607X-RAY DIFFRACTION98.48
2.33-2.410.31111340.2312568X-RAY DIFFRACTION99.78
2.41-2.490.28721420.22022631X-RAY DIFFRACTION99.78
2.49-2.590.29211370.22482613X-RAY DIFFRACTION99.93
2.59-2.710.31271450.21422597X-RAY DIFFRACTION99.67
2.71-2.850.22381350.20762596X-RAY DIFFRACTION98.91
2.85-3.030.24061430.20982627X-RAY DIFFRACTION100
3.03-3.260.28961430.21562630X-RAY DIFFRACTION99.93
3.26-3.590.26961380.20162629X-RAY DIFFRACTION99.6
3.59-4.110.21911490.17772669X-RAY DIFFRACTION99.47
4.11-5.180.19281420.15942698X-RAY DIFFRACTION99.86
5.18-46.820.2071610.17572818X-RAY DIFFRACTION99.53

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