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- PDB-5gul: Crystal structure of Tris/PPix2/Mg2+ bound form of cyclolavanduly... -

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Basic information

Entry
Database: PDB / ID: 5gul
TitleCrystal structure of Tris/PPix2/Mg2+ bound form of cyclolavandulyl diphosphate synthase (CLDS) from Streptomyces sp. CL190
ComponentsCyclolavandulyl diphosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / cyclolavandulyl diphosphate synthase / cis-prenyltransferase / Streptomyces sp. CL190 / Tris / PPi / Mg2+
Function / homologyditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / polyprenol biosynthetic process / Decaprenyl diphosphate synthase-like superfamily / metal ion binding / PYROPHOSPHATE 2- / Cyclolavandulyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsTomita, T. / Kobayashi, M. / Nishiyama, M. / Kuzuyama, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS26292058 Japan
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Structure and Mechanism of the Monoterpene Cyclolavandulyl Diphosphate Synthase that Catalyzes Consecutive Condensation and Cyclization.
Authors: Tomita, T. / Kobayashi, M. / Karita, Y. / Yasuno, Y. / Shinada, T. / Nishiyama, M. / Kuzuyama, T.
History
DepositionAug 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclolavandulyl diphosphate synthase
B: Cyclolavandulyl diphosphate synthase
C: Cyclolavandulyl diphosphate synthase
D: Cyclolavandulyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,69820
Polymers106,7044
Non-polymers1,99316
Water4,972276
1
A: Cyclolavandulyl diphosphate synthase
B: Cyclolavandulyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,34910
Polymers53,3522
Non-polymers9978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-23 kcal/mol
Surface area16910 Å2
MethodPISA
2
C: Cyclolavandulyl diphosphate synthase
D: Cyclolavandulyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,34910
Polymers53,3522
Non-polymers9978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-25 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.851, 61.661, 82.242
Angle α, β, γ (deg.)74.00, 84.54, 86.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cyclolavandulyl diphosphate synthase


Mass: 26676.123 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (strain CL190) (bacteria)
Strain: CL190 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: X5IYJ5
#2: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: H2O7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM HEPES NaOH pH 7.0, 24% PEG 2000

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→55.04 Å / Num. obs: 92115 / % possible obs: 85.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.1
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.434

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GUK

5guk


Resolution: 1.73→55.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.615 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27848 3967 5 %RANDOM
Rwork0.21555 ---
obs0.2187 75128 85.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.102 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20.01 Å20 Å2
2---0.01 Å2-0.01 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.73→55.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6812 0 108 276 7196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197060
X-RAY DIFFRACTIONr_bond_other_d0.0020.026516
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.9749556
X-RAY DIFFRACTIONr_angle_other_deg1.0883.00215012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2725860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53523.293328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.423151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1551552
X-RAY DIFFRACTIONr_chiral_restr0.1470.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217868
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021632
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1353.8113452
X-RAY DIFFRACTIONr_mcbond_other3.1353.8113451
X-RAY DIFFRACTIONr_mcangle_it3.9975.7114308
X-RAY DIFFRACTIONr_mcangle_other3.9965.7114309
X-RAY DIFFRACTIONr_scbond_it3.3984.0523608
X-RAY DIFFRACTIONr_scbond_other3.3974.0523609
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8995.9745249
X-RAY DIFFRACTIONr_long_range_B_refined6.09730.6778157
X-RAY DIFFRACTIONr_long_range_B_other6.09430.6258043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.726→1.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 309 -
Rwork0.335 5838 -
obs--90.18 %

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