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- PDB-3kro: Mint heterotetrameric geranyl pyrophosphate synthase in complex w... -

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Basic information

Entry
Database: PDB / ID: 3kro
TitleMint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium, IPP, and DMASPP (II)
Components(Geranyl diphosphate synthase ...) x 2
KeywordsTRANSFERASE / prenyltransferase / Isoprene biosynthesis / isoprenyl pyrophosphate synthase
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / farnesyltranstransferase activity / metal ion binding / cytoplasm
Similarity search - Function
: / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / PYROPHOSPHATE / Geranyl diphosphate synthase large subunit / Geranyl diphosphate synthase small subunit
Similarity search - Component
Biological speciesMentha x piperita (peppermint)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsChang, T.-H. / Hsieh, F.-L. / Ko, T.-P. / Wang, A.H.-J.
CitationJournal: Plant Cell / Year: 2010
Title: Structure of a heterotetrameric geranyl pyrophosphate synthase from mint (Mentha piperita) reveals intersubunit regulation
Authors: Chang, T.-H. / Hsieh, F.-L. / Ko, T.-P. / Teng, K.-H. / Liang, P.-H. / Wang, A.H.-J.
History
DepositionNov 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Oct 16, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Geranyl diphosphate synthase large subunit
B: Geranyl diphosphate synthase small subunit
C: Geranyl diphosphate synthase small subunit
D: Geranyl diphosphate synthase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,49813
Polymers123,4064
Non-polymers1,0929
Water20,2131122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Geranyl diphosphate synthase large subunit
B: Geranyl diphosphate synthase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1766
Polymers61,7032
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-37 kcal/mol
Surface area22290 Å2
MethodPISA
3
C: Geranyl diphosphate synthase small subunit
D: Geranyl diphosphate synthase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3227
Polymers61,7032
Non-polymers6195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-36 kcal/mol
Surface area21870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.441, 108.701, 182.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsGel filtration chromatography demonstrate that the biological assembly should be a hetero-tetramer, composed of two hetero-dimers (one is A chain and B chain, the other is C chain and D chain).

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Components

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Geranyl diphosphate synthase ... , 2 types, 4 molecules ADBC

#1: Protein Geranyl diphosphate synthase large subunit / GPPS Large Subunit / Geranyl pyrophosphate synthase large subunit / Gpp synthase large subunit


Mass: 31947.004 Da / Num. of mol.: 2 / Fragment: UNP residues 84-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mentha x piperita (peppermint) / Gene: GPPS Large Subunit / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9SBR3, dimethylallyltranstransferase
#2: Protein Geranyl diphosphate synthase small subunit / GPPS Small Subunit / Gpp synthase small subunit


Mass: 29755.963 Da / Num. of mol.: 2 / Fragment: UNP residues 49-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mentha x piperita (peppermint) / Gene: GPPS Small subunit / Plasmid: pET37 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9SBR4, dimethylallyltranstransferase

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Non-polymers , 6 types, 1131 molecules

#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1122 / 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: 2.15 Å3/Da / Density % sol: 42.66 % / Mosaicity: 0.634 °
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 100mM Bis-Tris, 200mM ammonium acetate, 20% PEG 3350, pH 6.5, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 29, 2008
RadiationMonochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 102519 / Num. obs: 76923 / % possible obs: 97.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.05 / Χ2: 1.067 / Net I/σ(I): 31.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3 / Num. unique all: 7460 / Χ2: 0.914 / % possible all: 95.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J1O

2j1o


Resolution: 1.95→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 5977 4.6 %RANDOM
Rwork0.205 ---
all0.232 76583 --
obs0.232 70606 90.1 %-
Solvent computationBsol: 64.287 Å2
Displacement parametersBiso max: 126.76 Å2 / Biso mean: 51.213 Å2 / Biso min: 22.68 Å2
Baniso -1Baniso -2Baniso -3
1--26.663 Å20 Å20 Å2
2--14.079 Å20 Å2
3---12.583 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8260 0 59 1122 9441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_d1.718
LS refinement shellResolution: 1.95→2.02 Å
RfactorNum. reflection
Rfree0.407 301
Rwork0.426 -
obs-5977
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4ligand.param

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