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- PDB-2vsn: Structure and topological arrangement of an O-GlcNAc transferase ... -

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Basic information

Entry
Database: PDB / ID: 2vsn
TitleStructure and topological arrangement of an O-GlcNAc transferase homolog: insight into molecular control of intracellular glycosylation
ComponentsXCOGT
KeywordsTRANSFERASE / GLYCOSYL TRANSFERASE / N- ACETYLGLUCOSAMINE / TPR / OGT / GLCNAC / O-GLYCOSYLATION
Function / homology
Function and homology information


protein O-GlcNAc transferase / glycosyltransferase activity / nucleotide binding
Similarity search - Function
: / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Glycogen Phosphorylase B; / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat ...: / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Glycogen Phosphorylase B; / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / protein O-GlcNAc transferase / TPR_REGION domain-containing protein
Similarity search - Component
Biological speciesXANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsMartinez-Fleites, C. / Macauley, M.S. / He, Y. / Shen, D. / Vocadlo, D. / Davies, G.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structure of an O-Glcnac Transferase Homolog Provides Insight Into Intracellular Glycosylation.
Authors: Martinez-Fleites, C. / Macauley, M.S. / He, Y. / Shen, D.L. / Vocadlo, D.J. / Davies, G.J.
History
DepositionApr 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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

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Assembly

Deposited unit
A: XCOGT
B: XCOGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4854
Polymers122,6772
Non-polymers8082
Water1,27971
1
A: XCOGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7432
Polymers61,3391
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: XCOGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7432
Polymers61,3391
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.691, 105.692, 151.036
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein XCOGT


Mass: 61338.570 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (bacteria)
Strain: 8004 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4URB5, UniProt: A0A0H2XAK3*PLUS, Transferases; Glycosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 290 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 290 TO ALA

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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: 2.88 Å3/Da / Density % sol: 0.57 % / Description: NONE
Crystal growDetails: 0.2M LI2SO4, 0.1M TRIS PH 8.5, 22.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.117 Å / Relative weight: 1
ReflectionResolution: 2.75→75.59 Å / Num. obs: 36765 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.75→75.52 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3302450.03 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1818 5 %RANDOM
Rwork0.241 ---
obs0.241 36717 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.4948 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--1.13 Å20 Å2
3----1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.75→75.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8113 0 50 71 8234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 296 4.9 %
Rwork0.353 5741 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2UDP_XPLOR_PAR.TXTION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMUDP_XPLOR_TOP.TXT

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