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

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Basic information

Entry
Database: PDB / ID: 6vyd
TitleTerpenoid Cyclase FgGS in Complex with Mg, Inorganic Pyrophosphate, and Benzyltriethylammonium cation
ComponentsTerpenoid cyclase FgGS
KeywordsLYASE / terpene / terpenoid / terpenoid cyclase
Function / homologyIsoprenoid synthase domain superfamily / N-benzyl-N,N-diethylethanaminium / PYROPHOSPHATE 2- / Chromosome 1, complete genome
Function and homology information
Biological speciesGibberella zeae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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
DepositionFeb 26, 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 11, 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 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,99842
Polymers72,3782
Non-polymers2,62040
Water9,134507
1
A: Terpenoid cyclase FgGS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,43219
Polymers36,1891
Non-polymers1,24318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Terpenoid cyclase FgGS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,56623
Polymers36,1891
Non-polymers1,37722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.599, 87.260, 163.209
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
11GLUGLULEULEU(chain 'A' and (resid 6 through 9 or (resid 10...AA6 - 276 - 27
12ARGARGGLUGLU(chain 'A' and (resid 6 through 9 or (resid 10...AA29 - 3329 - 33
13LEULEUTHRTHR(chain 'A' and (resid 6 through 9 or (resid 10...AA35 - 3835 - 38
14HISHISARGARG(chain 'A' and (resid 6 through 9 or (resid 10...AA41 - 4441 - 44
15ASPASPGLYGLY(chain 'A' and (resid 6 through 9 or (resid 10...AA46 - 5846 - 58
16ASNASNASNASN(chain 'A' and (resid 6 through 9 or (resid 10...AA6161
17ILEILELEULEU(chain 'A' and (resid 6 through 9 or (resid 10...AA63 - 7463 - 74
18PROPROGLUGLU(chain 'A' and (resid 6 through 9 or (resid 10...AA77 - 10077 - 100
19GLNGLNVALVAL(chain 'A' and (resid 6 through 9 or (resid 10...AA109 - 131109 - 131
110ALAALALYSLYS(chain 'A' and (resid 6 through 9 or (resid 10...AA133 - 138133 - 138
111TRPTRPLYSLYS(chain 'A' and (resid 6 through 9 or (resid 10...AA140 - 141140 - 141
112ALAALAILEILE(chain 'A' and (resid 6 through 9 or (resid 10...AA143 - 144143 - 144
113THRTHRLYSLYS(chain 'A' and (resid 6 through 9 or (resid 10...AA146 - 151146 - 151
114VALVALILEILE(chain 'A' and (resid 6 through 9 or (resid 10...AA153 - 158153 - 158
115TYRTYRVALVAL(chain 'A' and (resid 6 through 9 or (resid 10...AA161 - 174161 - 174
116ALAALAMETMET(chain 'A' and (resid 6 through 9 or (resid 10...AA176 - 184176 - 184
117LEULEUMETMET(chain 'A' and (resid 6 through 9 or (resid 10...AA186 - 234186 - 234
118ILEILELEULEU(chain 'A' and (resid 6 through 9 or (resid 10...AA236 - 239236 - 239
119ILEILEGLUGLU(chain 'A' and (resid 6 through 9 or (resid 10...AA241 - 256241 - 256
120GLUGLUTYRTYR(chain 'A' and (resid 6 through 9 or (resid 10...AA258 - 280258 - 280
121GLUGLUPROPRO(chain 'A' and (resid 6 through 9 or (resid 10...AA282 - 303282 - 303
222GLUGLULEULEU(chain 'B' and (resid 6 through 14 or (resid 15...BB6 - 276 - 27
223ARGARGGLUGLU(chain 'B' and (resid 6 through 14 or (resid 15...BB29 - 3329 - 33
224LEULEUTHRTHR(chain 'B' and (resid 6 through 14 or (resid 15...BB35 - 3835 - 38
225HISHISARGARG(chain 'B' and (resid 6 through 14 or (resid 15...BB41 - 4441 - 44
226ASPASPGLYGLY(chain 'B' and (resid 6 through 14 or (resid 15...BB46 - 5846 - 58
227ASNASNASNASN(chain 'B' and (resid 6 through 14 or (resid 15...BB6161
228ILEILELEULEU(chain 'B' and (resid 6 through 14 or (resid 15...BB63 - 7463 - 74
229PROPROGLUGLU(chain 'B' and (resid 6 through 14 or (resid 15...BB77 - 10077 - 100
230GLNGLNVALVAL(chain 'B' and (resid 6 through 14 or (resid 15...BB109 - 131109 - 131
231ALAALALYSLYS(chain 'B' and (resid 6 through 14 or (resid 15...BB133 - 138133 - 138
232TRPTRPLYSLYS(chain 'B' and (resid 6 through 14 or (resid 15...BB140 - 141140 - 141
233ALAALAILEILE(chain 'B' and (resid 6 through 14 or (resid 15...BB143 - 144143 - 144
234THRTHRLYSLYS(chain 'B' and (resid 6 through 14 or (resid 15...BB146 - 151146 - 151
235VALVALILEILE(chain 'B' and (resid 6 through 14 or (resid 15...BB153 - 158153 - 158
236TYRTYRVALVAL(chain 'B' and (resid 6 through 14 or (resid 15...BB161 - 174161 - 174
237ALAALAMETMET(chain 'B' and (resid 6 through 14 or (resid 15...BB176 - 184176 - 184
238LEULEUMETMET(chain 'B' and (resid 6 through 14 or (resid 15...BB186 - 234186 - 234
239ILEILELEULEU(chain 'B' and (resid 6 through 14 or (resid 15...BB236 - 239236 - 239
240ILEILEGLUGLU(chain 'B' and (resid 6 through 14 or (resid 15...BB241 - 256241 - 256
241GLUGLUTYRTYR(chain 'B' and (resid 6 through 14 or (resid 15...BB258 - 280258 - 280
242GLUGLUPROPRO(chain 'B' and (resid 6 through 14 or (resid 15...BB282 - 303282 - 303

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Components

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Protein , 1 types, 2 molecules AB

#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, 547 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H22N / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL FgGS, 2 mM BTAC, 10 mM magnesium chloride, 2 mM sodium pyrophosphate, 0.2 M NaCl, 0.1 M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.46→46.17 Å / Num. obs: 118843 / % possible obs: 98.3 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.043 / Net I/σ(I): 11.2
Reflection shellResolution: 1.46→1.51 Å / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 11626 / CC1/2: 0.67 / Rpim(I) all: 0.567

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Processing

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

5ert


Resolution: 1.46→46.17 Å / SU ML: 0.152 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.5123 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1838 6038 5.08 %
Rwork0.1496 112787 -
obs0.1513 118825 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.53 Å2
Refinement stepCycle: LAST / Resolution: 1.46→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 158 507 5359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01045048
X-RAY DIFFRACTIONf_angle_d1.08196830
X-RAY DIFFRACTIONf_chiral_restr0.0783755
X-RAY DIFFRACTIONf_plane_restr0.007875
X-RAY DIFFRACTIONf_dihedral_angle_d23.16541878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.480.30272070.25083678X-RAY DIFFRACTION97
1.48-1.490.29351710.24653677X-RAY DIFFRACTION97.07
1.49-1.510.30941970.23243694X-RAY DIFFRACTION97.2
1.51-1.530.25271870.21083706X-RAY DIFFRACTION97.3
1.53-1.550.222200.19453635X-RAY DIFFRACTION97.47
1.55-1.570.22881970.18373758X-RAY DIFFRACTION97.53
1.57-1.60.24622150.18143656X-RAY DIFFRACTION97.73
1.6-1.620.21891920.16993734X-RAY DIFFRACTION97.76
1.62-1.640.19931850.15973705X-RAY DIFFRACTION97.91
1.64-1.670.19122100.15073745X-RAY DIFFRACTION97.92
1.67-1.70.19671850.14263707X-RAY DIFFRACTION97.99
1.7-1.730.19771910.13813766X-RAY DIFFRACTION98.29
1.73-1.760.18862010.13363711X-RAY DIFFRACTION98.17
1.76-1.80.19131680.14483795X-RAY DIFFRACTION98.36
1.8-1.840.20331930.14273757X-RAY DIFFRACTION98.43
1.84-1.880.20612170.13473761X-RAY DIFFRACTION98.54
1.88-1.930.19012170.13633744X-RAY DIFFRACTION98.61
1.93-1.980.21451880.13563402X-RAY DIFFRACTION89.44
1.98-2.040.19242070.1333739X-RAY DIFFRACTION97.46
2.04-2.110.18252020.13013797X-RAY DIFFRACTION98.89
2.11-2.180.16411950.12773789X-RAY DIFFRACTION99.03
2.18-2.270.17912120.13073774X-RAY DIFFRACTION99.13
2.27-2.370.17422300.12993810X-RAY DIFFRACTION99.34
2.37-2.50.16631830.13553859X-RAY DIFFRACTION99.48
2.5-2.650.19251940.14283845X-RAY DIFFRACTION99.43
2.65-2.860.18142080.14533884X-RAY DIFFRACTION99.61
2.86-3.150.1892030.1553867X-RAY DIFFRACTION99.71
3.15-3.60.18531790.16033872X-RAY DIFFRACTION98.44
3.6-4.540.15182200.14083832X-RAY DIFFRACTION96.66
4.54-46.580.17172640.16434088X-RAY DIFFRACTION99.75

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