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- PDB-5hc6: Crystal structure of lavandulyl diphosphate synthase from Lavandu... -

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Basic information

Entry
Database: PDB / ID: 5hc6
TitleCrystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in apo form
Componentsprenyltransference for protein
KeywordsTRANSFERASE / substrate binding / lavandulyl
Function / homology
Function and homology information


plastid membrane organization / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / chloroplast stroma / response to cold / metal ion binding
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesLavandula lanata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLiu, M.X. / Liu, W.D. / Gao, J. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Structure and Function of a "Head-to-Middle" Prenyltransferase: Lavandulyl Diphosphate Synthase
Authors: Liu, M.X. / Chen, C.C. / Chen, L. / Xiao, X.S. / Zheng, Y.Y. / Huang, J.W. / Liu, W.D. / Ko, T.P. / Cheng, Y.S. / Feng, X.X. / Oldfield, E. / Guo, R.T. / Ma, Y.H.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: prenyltransference for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0404
Polymers29,7521
Non-polymers2883
Water93752
1
A: prenyltransference for protein
hetero molecules

A: prenyltransference for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0808
Polymers59,5032
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area4570 Å2
ΔGint-113 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.357, 142.085, 78.666
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-546-

HOH

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Components

#1: Protein prenyltransference for protein


Mass: 29751.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lavandula lanata (plant) / Plasmid: pET46Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A140UHQ1*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium Sulfate, Glycerol, PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. obs: 16659 / % possible obs: 98 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Rrim(I) all: 0.064 / Χ2: 1.098 / Net I/av σ(I): 22.353 / Net I/σ(I): 11.3 / Num. measured all: 58377
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.233.40.41815690.8550.250.490.96193.5
2.23-2.323.50.32916480.9290.1970.3860.94998.4
2.32-2.423.60.2616510.9350.1570.3060.98399.8
2.42-2.553.60.19216800.9640.1150.2251.02299.6
2.55-2.713.60.1516800.9780.090.1761.08899.6
2.71-2.923.60.10216770.9910.0610.121.11599.1
2.92-3.213.50.06716650.9950.040.0791.16698.9
3.21-3.673.50.04716760.9970.0280.0541.23498.3
3.67-4.623.30.04216960.9970.0260.0491.15498
4.62-253.50.02817170.9990.0170.0331.30794.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.2271 / WRfactor Rwork: 0.1776 / FOM work R set: 0.7766 / SU B: 6.479 / SU ML: 0.159 / SU R Cruickshank DPI: 0.1916 / SU Rfree: 0.1795 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 814 4.9 %RANDOM
Rwork0.1792 ---
obs0.1819 15828 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.69 Å2 / Biso mean: 49.902 Å2 / Biso min: 27.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å20 Å2
2--4.19 Å20 Å2
3----2.79 Å2
Refinement stepCycle: final / Resolution: 2.15→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 15 52 1920
Biso mean--67.01 53.32 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191908
X-RAY DIFFRACTIONr_bond_other_d0.0010.021805
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9512583
X-RAY DIFFRACTIONr_angle_other_deg0.91234142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0825229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.43523.85496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33715327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4181514
X-RAY DIFFRACTIONr_chiral_restr0.1290.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
X-RAY DIFFRACTIONr_mcbond_it3.6284.589919
X-RAY DIFFRACTIONr_mcbond_other3.5874.588918
X-RAY DIFFRACTIONr_mcangle_it4.9566.8681147
LS refinement shellResolution: 2.149→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 52 -
Rwork0.278 1060 -
all-1112 -
obs--90.55 %

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