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- PDB-5ax7: yeast pyruvyltransferase Pvg1p -

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Basic information

Entry
Database: PDB / ID: 5ax7
Titleyeast pyruvyltransferase Pvg1p
ComponentsPyruvyl transferase 1
KeywordsTRANSFERASE / pyruvylation
Function / homology
Function and homology information


pyruvyltransferase activity / 4,6-pyruvylated galactose residue biosynthetic process / Transferases / fungal-type cell wall biogenesis / cell wall organization / Golgi apparatus / cytoplasm
Similarity search - Function
Polysaccharide pyruvyl transferase / Polysaccharide pyruvyl transferase
Similarity search - Domain/homology
Pyruvyl transferase 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsKanekiyo, M. / Yoritsune, K. / Yoshinaga, S. / Higuchi, Y. / Takegawa, K. / Kakuta, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
a Grant-in-Aid for Scientific Research from the Ministry of Education, Science, and Culture of Japan Japan
CitationJournal: Sci Rep / Year: 2016
Title: A rationally engineered yeast pyruvyltransferase Pvg1p introduces sialylation-like properties in neo-human-type complex oligosaccharide
Authors: Higuchi, Y. / Yoshinaga, S. / Yoritsune, K. / Tateno, H. / Hirabayashi, J. / Nakakita, S. / Kanekiyo, M. / Kakuta, Y. / Takegawa, K.
History
DepositionJul 16, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr2_symmetry / _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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvyl transferase 1
B: Pyruvyl transferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2773
Polymers78,2112
Non-polymers651
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-30 kcal/mol
Surface area27620 Å2
Unit cell
Length a, b, c (Å)85.529, 85.529, 93.611
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 55 - 401 / Label seq-ID: 2 - 348

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Pyruvyl transferase 1 / Pyruvylated Gal-beta-1 / 3-epitope synthesis protein 1 / PvGal synthesis protein 1


Mass: 39105.719 Da / Num. of mol.: 2 / Fragment: UNP residues 54-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: pvg1, SPAC8F11.10c, SPACUNK4.18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UT27, Transferases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 293.4 K / Method: vapor diffusion, sitting drop
Details: 200 mM magnesium choloride, 10 mM zinc chloride, 26% (w/v) Poly(acrylic acid sodium salt) 5100 in 0.1 M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.3 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.722
11K, H, -L20.278
ReflectionResolution: 2.46→10.99 Å / Num. obs: 55667 / % possible obs: 99.8 % / Redundancy: 5.77 % / Net I/σ(I): 25.14

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHENIXrefinement
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.46→10.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.868 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18335 1461 5.3 %RANDOM
Rwork0.1673 ---
obs0.16814 26299 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.694 Å2
Baniso -1Baniso -2Baniso -3
1--5.63 Å20 Å20 Å2
2---5.63 Å20 Å2
3---11.25 Å2
Refinement stepCycle: 1 / Resolution: 2.46→10.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 1 67 5311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195397
X-RAY DIFFRACTIONr_bond_other_d0.0020.025022
X-RAY DIFFRACTIONr_angle_refined_deg0.9591.9457366
X-RAY DIFFRACTIONr_angle_other_deg0.861311546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3725662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8524.402259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1715845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4831524
X-RAY DIFFRACTIONr_chiral_restr0.0580.2827
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216148
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021274
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_it1.5185.3332648
X-RAY DIFFRACTIONr_mcbond_other1.5175.3322647
X-RAY DIFFRACTIONr_mcangle_it2.6257.9893304
X-RAY DIFFRACTIONr_mcangle_other2.6257.993305
X-RAY DIFFRACTIONr_scbond_it1.2835.4622749
X-RAY DIFFRACTIONr_scbond_other1.2835.4632750
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.258.1424061
X-RAY DIFFRACTIONr_long_range_B_refined4.07842.2336005
X-RAY DIFFRACTIONr_long_range_B_other4.07142.2366001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 19109 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 107 -
Rwork0.244 1949 -
obs--99.52 %

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