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- PDB-2xgm: Substrate and product analogues as human O-GlcNAc transferase inh... -

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Basic information

Entry
Database: PDB / ID: 2xgm
TitleSubstrate and product analogues as human O-GlcNAc transferase inhibitors.
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
ALLOXAN / protein O-GlcNAc transferase
Similarity search - Component
Biological speciesXANTHOMONAS CAMPESTRIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.55 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 12, 2011Group: Database references / Version format compliance
Revision 1.2May 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)123,1344
Polymers122,8492
Non-polymers2842
Water1,04558
1
A: XCOGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5672
Polymers61,4251
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: XCOGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5672
Polymers61,4251
Non-polymers1421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.534, 99.982, 157.196
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-LXN / ALLOXAN / MESOXALYLUREA


Mass: 142.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H2N2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 0.1MCHES, PH 9.5, 25% POLYETHYLENEGLYCOL 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 42658 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.3

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.55→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 38.921 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R: 0.66 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1334 3.1 %RANDOM
Rwork0.267 ---
obs0.268 41266 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8018 0 20 58 8096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0218267
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.94811288
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.69551056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00822.347375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.115151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.751581
X-RAY DIFFRACTIONr_chiral_restr0.1090.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216499
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_it0.4621.55265
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79728361
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.11933002
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6054.52926
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: 3886 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.080.05
2Btight positional0.080.05
1Atight thermal0.130.5
2Btight thermal0.130.5
LS refinement shellResolution: 2.55→2.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 86 -
Rwork0.371 2899 -
obs--100 %
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)
10.75720.4493-0.27621.99310.09452.72010.22490.08710.05680.1855-0.1970.484-0.1205-0.9991-0.02790.3159-0.04210.05270.4202-0.0380.572710.227.015-4.661
22.51060.3776-0.53722.96170.09023.68980.15510.0016-0.22050.00230.1157-0.587-0.49320.7852-0.27080.198-0.12660.0950.1767-0.08620.400836.1218.602-8.625
31.23870.17430.162.0039-1.52074.2267-0.00810.0687-0.2675-0.5337-0.192-0.38980.63781.57310.20010.81570.0147-0.02430.7170.07930.570632.637-0.61527.735
43.4327-0.00150.81052.52570.65055.6624-0.32140.05760.4323-0.84820.04910.6373-1.7505-0.48920.27231.12250.1893-0.3480.14450.03740.534512.36615.3732.464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 300
2X-RAY DIFFRACTION2A320 - 568
3X-RAY DIFFRACTION3B22 - 300
4X-RAY DIFFRACTION4B320 - 568
5X-RAY DIFFRACTION4A1569
6X-RAY DIFFRACTION4B1569

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