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- PDB-3oac: Mint deletion mutant of heterotetrameric geranyl pyrophosphate sy... -

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Basic information

Entry
Database: PDB / ID: 3oac
TitleMint deletion mutant of heterotetrameric geranyl pyrophosphate synthase in complex with ligands
Components(Geranyl diphosphate synthase ...) x 2
KeywordsTRANSFERASE / prenyltransferase / All alpha-helices fold / prenyltransferase and monoterpene biosynthesis / chroloplast
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / metal ion binding
Similarity search - Function
Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / 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 / Geranyl diphosphate synthase large subunit / Geranyl diphosphate synthase small subunit
Similarity search - Component
Biological speciesMentha x piperita (peppermint)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Enhanced specificity of mint geranyl pyrophosphate synthase by modifying the R-loop interactions
Authors: Hsieh, F.-L. / Chang, T.-H. / Ko, T.-P. / Wang, A.H.-J.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 8, 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_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_seq_id / _struct_conn.ptnr2_label_asym_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: 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)121,8768
Polymers121,3204
Non-polymers5574
Water3,027168
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


Theoretical massNumber of molelcules
Total (without water)60,6602
Polymers60,6602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-37 kcal/mol
Surface area22000 Å2
MethodPISA
3
C: Geranyl diphosphate synthase small subunit
D: Geranyl diphosphate synthase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2176
Polymers60,6602
Non-polymers5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-36 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.842, 110.110, 111.500
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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Geranyl diphosphate synthase ... , 2 types, 4 molecules ADBC

#1: Protein Geranyl diphosphate synthase 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) / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9SBR3, dimethylallyltranstransferase
#2: Protein Geranyl diphosphate synthase small subunit / Gpp synthase small subunit


Mass: 28712.795 Da / Num. of mol.: 2 / Fragment: UNP residues 49-313 / Mutation: DELETION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mentha x piperita (peppermint) / Plasmid: pET37 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9SBR4, dimethylallyltranstransferase

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Non-polymers , 4 types, 172 molecules

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


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate / Dimethylallyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
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 315 / Detector: CCD / Date: Jan 20, 2009
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: 2.6→30 Å / Num. obs: 33831 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3208 / % possible all: 91.3

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KRF

3krf


Resolution: 2.6→26.28 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1596 4.5 %RANDOM
Rwork0.2025 ---
all-33831 --
obs-32124 89.7 %-
Solvent computationBsol: 34.7116 Å2
Displacement parametersBiso max: 125.26 Å2 / Biso mean: 42.1895 Å2 / Biso min: 10.46 Å2
Baniso -1Baniso -2Baniso -3
1-10.761 Å20 Å20 Å2
2--9.993 Å20 Å2
3----20.754 Å2
Refinement stepCycle: LAST / Resolution: 2.6→26.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8098 0 30 168 8296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_d2.062
LS refinement shellResolution: 2.6→2.69 Å
RfactorNum. reflection% reflection
Rfree0.369 133 -
Rwork0.276 --
obs-2780 89.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4ligand.param

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