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- PDB-5a07: X-ray structure of the mannosyltransferase Ktr4p from S. cerevisi... -

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Basic information

Entry
Database: PDB / ID: 5a07
TitleX-ray structure of the mannosyltransferase Ktr4p from S. cerevisiae in complex with GDP
ComponentsPROBABLE MANNOSYLTRANSFERASE KTR4
KeywordsTRANSFERASE / GOLGI APPARATUS / MANNOSYLTRANSFERASES / GT-A / MEMBRANE PROTEINS
Function / homology
Function and homology information


alpha-1,2-mannosyltransferase activity / mannosylation / mannosyltransferase activity / cell wall mannoprotein biosynthetic process / fungal-type vacuole / protein O-linked glycosylation / protein N-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi apparatus / membrane
Similarity search - Function
Glycosyl transferase, family 15 / Glycolipid 2-alpha-mannosyltransferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-DIPHOSPHATE / : / Probable mannosyltransferase KTR4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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.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_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_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_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

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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)103,5678
Polymers102,4532
Non-polymers1,1146
Water10,413578
1
B: PROBABLE MANNOSYLTRANSFERASE KTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7844
Polymers51,2261
Non-polymers5573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: PROBABLE MANNOSYLTRANSFERASE KTR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7844
Polymers51,2261
Non-polymers5573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.215, 102.621, 162.651
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: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 71 - 463 / Label seq-ID: 41 - 433

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

NCS oper: (Code: given
Matrix: (0.7457, 0.6628, 0.06883), (0.6626, -0.7484, 0.02793), (0.07002, 0.02478, -0.9972)
Vector: -11.77, 34.73, -35.09)

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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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.5 Å3/Da / Density % sol: 50.75 % / 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: 0.972422
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Jun 18, 2014 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 81509 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2.3 / % possible all: 98.9

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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 5A08

5a08


Resolution: 1.9→86.79 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.919 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19132 3941 4.9 %RANDOM
Rwork0.15627 ---
obs0.15798 76662 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.426 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20 Å2
2---1.67 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.9→86.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 66 578 7250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196901
X-RAY DIFFRACTIONr_bond_other_d0.0070.026027
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.959391
X-RAY DIFFRACTIONr_angle_other_deg1.258313947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19225.038395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2351528
X-RAY DIFFRACTIONr_chiral_restr0.1180.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217914
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021686
X-RAY DIFFRACTIONr_nbd_refined0.2760.22143
X-RAY DIFFRACTIONr_nbd_other0.1890.26155
X-RAY DIFFRACTIONr_nbtor_refined0.1960.23457
X-RAY DIFFRACTIONr_nbtor_other0.0860.23289
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0370.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3880.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3862.3793167
X-RAY DIFFRACTIONr_mcbond_other2.3852.3793164
X-RAY DIFFRACTIONr_mcangle_it3.1113.5533956
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8182.7563734
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8233.9725432
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: 23881 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 277 -
Rwork0.273 5551 -
obs--98.65 %

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