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- PDB-5hc8: Crystal structure of lavandulyl diphosphate synthase from Lavandu... -

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Basic information

Entry
Database: PDB / ID: 5hc8
TitleCrystal structure of lavandulyl diphosphate synthase from Lavandula x intermedia in complex with dimethylallyl diphosphate
Componentsprenyltransference for protein
KeywordsTRANSFERASE / substrate binding / prenyltransferase / substrate
Function / homology
Function and homology information


plastid membrane organization / dehydrodolichyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / 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
2-methylbuta-1,3-diene / Chem-ISY / TRIHYDROGEN THIODIPHOSPHATE / Alkyl transferase
Similarity search - Component
Biological speciesLavandula lanata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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.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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prenyltransference for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3956
Polymers29,7521
Non-polymers6445
Water2,450136
1
A: prenyltransference for protein
hetero molecules

A: prenyltransference for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,79112
Polymers59,5032
Non-polymers1,28710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area5520 Å2
ΔGint-75 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.211, 140.235, 78.702
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 141 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PIS / TRIHYDROGEN THIODIPHOSPHATE / THIOPYROPHOSPHATE


Mass: 193.033 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3O6P2S
#4: Chemical ChemComp-61G / 2-methylbuta-1,3-diene


Mass: 68.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ISY / 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid / Isopentyl S-Thiolodiphosphate


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


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
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: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 25038 / % possible obs: 99 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.021 / Rrim(I) all: 0.045 / Χ2: 0.988 / Net I/av σ(I): 26.064 / Net I/σ(I): 18.8 / Num. measured all: 111471
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.87-1.944.20.34924070.9370.190.41.15996.9
1.94-2.014.50.27524840.9530.1460.3131.132100
2.01-2.114.50.20924820.9720.110.2381.169100
2.11-2.224.50.14925100.9840.0780.1691.05799.9
2.22-2.364.60.10725100.9910.0560.1221.10799.9
2.36-2.544.50.08825040.9940.0460.11.08499.9
2.54-2.794.50.06425220.9960.0330.0720.98499.8
2.79-3.24.50.03725270.9990.0190.0410.61299.4
3.2-4.034.40.02825070.9990.0150.0320.64698.1
4.03-504.30.01925850.9990.010.0210.9596.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V7U

1v7u


Resolution: 1.87→25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.1819 / FOM work R set: 0.8187 / SU B: 3.421 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1193 / SU Rfree: 0.1206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 1276 5.1 %RANDOM
Rwork0.1707 ---
obs0.1729 23751 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.61 Å2 / Biso mean: 38.321 Å2 / Biso min: 18.84 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å20 Å2
2--3.17 Å20 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 1.87→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 34 137 2075
Biso mean--37.33 45.29 -
Num. residues----236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021978
X-RAY DIFFRACTIONr_bond_other_d0.0020.021864
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9592677
X-RAY DIFFRACTIONr_angle_other_deg1.0613.0014270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10123.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.43515334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5511515
X-RAY DIFFRACTIONr_chiral_restr0.1550.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212230
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02487
X-RAY DIFFRACTIONr_mcbond_it3.173.45943
X-RAY DIFFRACTIONr_mcbond_other3.173.448942
X-RAY DIFFRACTIONr_mcangle_it4.355.1591177
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 85 -
Rwork0.269 1705 -
all-1790 -
obs--98.41 %

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