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- PDB-5a08: X-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5a08
TitleX-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae
ComponentsPROBABLE MANNOSYLTRANSFERASE KTR4
KeywordsTRANSFERASE / GOLGI APPARATUS / MANNOSYLTRANSFERASES / GT-A / MEMBRANE PROTEINS
Function / homology
Function and homology information


alpha-1,2-mannosyltransferase activity / mannosyltransferase activity / cell wall mannoprotein biosynthetic process / protein O-linked glycosylation / fungal-type vacuole / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi apparatus / membrane
Similarity search - Function
Glycosyl transferase, family 15 / Glycolipid 2-alpha-mannosyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Probable mannosyltransferase KTR4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPossner, D.D.D. / Guy, J.E.
CitationJournal: Plos One / Year: 2015
Title: Structure of the Glycosyltransferase Ktr4P from Saccharomyces Cerevisiae
Authors: Possner, D.D.D. / Claesson, M. / Guy, J.E.
History
DepositionApr 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE MANNOSYLTRANSFERASE KTR4
B: PROBABLE MANNOSYLTRANSFERASE KTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6917
Polymers102,4532
Non-polymers2385
Water8,971498
1
B: PROBABLE MANNOSYLTRANSFERASE KTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4065
Polymers51,2261
Non-polymers1794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: PROBABLE MANNOSYLTRANSFERASE KTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2852
Polymers51,2261
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.198, 102.368, 156.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 71 - 464 / Label seq-ID: 41 - 434

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

NCS oper: (Code: given
Matrix: (0.7453, 0.6631, 0.0689), (0.663, -0.7481, 0.02776), (0.06996, 0.02499, -0.9972)
Vector: -11.8, 34.74, -35.1)

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Components

#1: Protein PROBABLE MANNOSYLTRANSFERASE KTR4 / KTR4P


Mass: 51226.426 Da / Num. of mol.: 2 / Fragment: LUMENAL PART, RESIDUES 33-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ROSETTA-GAMI 2
References: UniProt: P38131, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.95 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M NA-CACODYLATE, PH 6.5 0.2M CAOAC 18% (W/V) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: May 17, 2014 / Details: KB MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 49674 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S4N

1s4n


Resolution: 2.21→85.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.68 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20273 2420 4.9 %RANDOM
Rwork0.16311 ---
obs0.16502 47109 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.972 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.21→85.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6538 0 11 498 7047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196785
X-RAY DIFFRACTIONr_bond_other_d0.0060.025960
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9379224
X-RAY DIFFRACTIONr_angle_other_deg1.122313789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92125.038393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.707151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1181528
X-RAY DIFFRACTIONr_chiral_restr0.1020.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217821
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021667
X-RAY DIFFRACTIONr_nbd_refined0.2770.22254
X-RAY DIFFRACTIONr_nbd_other0.1950.26370
X-RAY DIFFRACTIONr_nbtor_refined0.2020.23489
X-RAY DIFFRACTIONr_nbtor_other0.0880.23333
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.080.23
X-RAY DIFFRACTIONr_metal_ion_refined0.4610.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3930.245
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4460.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1112.3053137
X-RAY DIFFRACTIONr_mcbond_other2.1112.3053134
X-RAY DIFFRACTIONr_mcangle_it3.0823.4473917
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.122.5863648
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.823.7515300
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23965 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 181 -
Rwork0.233 3293 -
obs--96.26 %

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