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- PDB-2xgs: XcOGT in complex with C-UDP -

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Basic information

Entry
Database: PDB / ID: 2xgs
TitleXcOGT in complex with C-UDP
ComponentsXCOGT
KeywordsTRANSFERASE
Function / homology
Function and homology information


protein O-GlcNAc transferase / glycosyltransferase activity / metal ion binding
Similarity search - Function
Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Glycogen Phosphorylase B; / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Glycogen Phosphorylase B; / 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
Chem-44P / protein O-GlcNAc transferase
Similarity search - Component
Biological speciesXANTHOMONAS CAMPESTRIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsDorfmueller, H.C. / Borodkin, V.S. / Blair, D.E. / Pathak, S. / Navratilova, I. / van Aalten, D.M.
CitationJournal: Amino Acids / Year: 2011
Title: Substrate and Product Analogues as Human O-Glcnac Transferase Inhibitors.
Authors: Dorfmueller, H.C. / Borodkin, V.S. / Blair, D.E. / Pathak, S. / Navratilova, I. / Van Aalten, D.M.
History
DepositionJun 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: 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 / 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

Downloads & links

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Assembly

Deposited unit
A: XCOGT
B: XCOGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6544
Polymers122,8492
Non-polymers8042
Water1,49583
1
A: XCOGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8272
Polymers61,4251
Non-polymers4021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: XCOGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8272
Polymers61,4251
Non-polymers4021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.286, 94.980, 157.655
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
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A40 - 568
2111B40 - 568

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Components

#1: Protein XCOGT


Mass: 61424.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XANTHOMONAS CAMPESTRIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q8PC69
#2: Chemical ChemComp-44P / 5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 0.1 M CHES, PH 9.5, 25% POLYETHYLENEGLYCOL 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 47424 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.6
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.15 / % possible all: 70.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JLB

2jlb


Resolution: 2.39→19.87 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.856 / SU B: 23.613 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-26 IN CHAIN A AND 1-89 IN CHAIN B ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.316 965 2 %RANDOM
Rwork0.257 ---
obs0.258 46221 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.39→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 50 83 7901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0218024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.95610962
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.69551019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94622.333360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.58151155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2581577
X-RAY DIFFRACTIONr_chiral_restr0.1190.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216275
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6031.55090
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13628083
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81532934
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9014.52879
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: 3651 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.090.05
2Btight positional0.090.05
1Atight thermal0.180.5
2Btight thermal0.180.5
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 62 -
Rwork0.343 2659 -
obs--74.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04630.0698-0.0930.621-0.10780.28450.00260.0308-0.01340.01950.01820.08730.0078-0.0766-0.02080.0375-0.0102-0.01360.026-0.00470.0588-31.44095.571-3.909
20.4255-0.1550.0060.3463-0.01720.24270.01940.0291-0.0536-0.0130.0039-0.0378-0.00360.0435-0.02330.0382-0.0025-0.01390.0106-0.00980.0401-6.26617.309-7.9384
30.3330.14770.02280.47380.04910.38780.0396-0.0361-0.0188-0.0123-0.02270.01020.04430.1368-0.01690.04310.0099-0.00280.05880.00170.0126-10.50735.211531.6832
40.44470.032-0.01060.1579-0.00180.4940.0561-0.03060.02560.030.02760.0565-0.0751-0.0629-0.08370.03750.00130.02010.02170.02220.0356-29.880214.060932.4373
5-0.19090.002-0.4113-0.36570.2532-1.51630.1001-0.0158-0.0347-0.0772-0.0235-0.0034-0.06040.0187-0.07660.7988-0.1532-0.04530.0754-0.01210.1097-13.51257.24220.1778
61.94642.25972.32847.4884-4.660113.42170.26050.38620.04240.31480.53120.61640.21410.3534-0.79170.09420.0070.02270.10680.00840.0686-23.538610.392324.5657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 300
2X-RAY DIFFRACTION2A320 - 568
3X-RAY DIFFRACTION3B28 - 300
4X-RAY DIFFRACTION4B320 - 568
5X-RAY DIFFRACTION5A1569
6X-RAY DIFFRACTION6B1569

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