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- PDB-5e8h: Crystal structure of geranylfarnesyl pyrophosphate synthases 2 fr... -

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Basic information

Entry
Database: PDB / ID: 5e8h
TitleCrystal structure of geranylfarnesyl pyrophosphate synthases 2 from Arabidopsis thaliana
ComponentsGeranylgeranyl pyrophosphate synthase 3, chloroplastic
KeywordsTRANSFERASE / GFPPS / prenyltransferase
Function / homology
Function and homology information


carotenoid biosynthetic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity ...carotenoid biosynthetic process / geranylgeranyl diphosphate biosynthetic process / geranylgeranyl diphosphate synthase / farnesyltranstransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / chloroplast / 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
Geranylgeranyl pyrophosphate synthase 3, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsWang, C. / Chen, Q. / Wang, G. / Zhang, P.
CitationJournal: Mol Plant / Year: 2016
Title: Structural Analyses of Short-Chain Prenyltransferases Identify an Evolutionarily Conserved GFPPS Clade in Brassicaceae Plants.
Authors: Wang, C. / Chen, Q. / Fan, D. / Li, J. / Wang, G. / Zhang, P.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geranylgeranyl pyrophosphate synthase 3, chloroplastic
B: Geranylgeranyl pyrophosphate synthase 3, chloroplastic


Theoretical massNumber of molelcules
Total (without water)71,6572
Polymers71,6572
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-44 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.245, 77.090, 114.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Geranylgeranyl pyrophosphate synthase 3, chloroplastic / GGPS3 / (2E / 6E)-farnesyl diphosphate synthase 3 / Dimethylallyltranstransferase 3 / Farnesyl ...GGPS3 / (2E / 6E)-farnesyl diphosphate synthase 3 / Dimethylallyltranstransferase 3 / Farnesyl diphosphate synthase 3 / Farnesyltranstransferase 3 / Geranyltranstransferase 3


Mass: 35828.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GGPP3, At3g14550, MIE1.5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LUD9, Transferases; Transferring alkyl or aryl groups, other than methyl groups, dimethylallyltranstransferase, geranylgeranyl diphosphate synthase, (2E,6E)-farnesyl diphosphate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.0 M ammonium sulfate, 2% PEG 400, pH7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 28044 / % possible obs: 90.1 % / Redundancy: 4.6 % / Net I/σ(I): 28.3

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementResolution: 2.3→36.52 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 1399 4.99 %
Rwork0.2069 --
obs0.2082 28044 89.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4127 0 0 259 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014178
X-RAY DIFFRACTIONf_angle_d1.4735645
X-RAY DIFFRACTIONf_dihedral_angle_d14.461545
X-RAY DIFFRACTIONf_chiral_restr0.06683
X-RAY DIFFRACTIONf_plane_restr0.005723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2886-2.37040.22751420.21662542X-RAY DIFFRACTION86
2.3704-2.46530.24541490.20822809X-RAY DIFFRACTION95
2.4653-2.57750.24781560.21982778X-RAY DIFFRACTION95
2.5775-2.71330.25981370.22522800X-RAY DIFFRACTION95
2.7133-2.88320.25731350.22522809X-RAY DIFFRACTION94
2.8832-3.10570.24181400.22972782X-RAY DIFFRACTION94
3.1057-3.41810.2881530.22832770X-RAY DIFFRACTION93
3.4181-3.91220.21851260.20382163X-RAY DIFFRACTION72
3.9122-4.9270.17991240.1672642X-RAY DIFFRACTION87
4.927-36.52460.2241370.1982550X-RAY DIFFRACTION81
Refinement TLS params.Method: refined / Origin x: 22.9888 Å / Origin y: 88.6908 Å / Origin z: 129.2486 Å
111213212223313233
T0.13 Å2-0.021 Å20.0035 Å2-0.1585 Å20.0033 Å2--0.1185 Å2
L0.6572 °2-0.4847 °20.1639 °2-1.4471 °2-0.2568 °2--0.5361 °2
S-0.0396 Å °-0.0443 Å °-0.0246 Å °-0.0053 Å °0.0505 Å °0.078 Å °0.0042 Å °-0.078 Å °-0.0083 Å °
Refinement TLS groupSelection details: all

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