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- PDB-2vsy: Xanthomonas campestris putative OGT (XCC0866), apostructure -

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Basic information

Entry
Database: PDB / ID: 2vsy
TitleXanthomonas campestris putative OGT (XCC0866), apostructure
ComponentsXCC0866
KeywordsTRANSFERASE / GLYCOSYL TRANSFERASE / GT-B / OGT / PROTEIN O-GLCNACYLATION
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
DI(HYDROXYETHYL)ETHER / PRASEODYMIUM ION / protein O-GlcNAc transferase
Similarity search - Component
Biological speciesXANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchuettelkopf, A.W. / Clarke, A.J. / van Aalten, D.M.F.
CitationJournal: Embo J. / Year: 2008
Title: Structural Insights Into Mechanism and Specificity of O-Glcnac Transferase.
Authors: Clarke, A.J. / Hurtado-Guerrero, R. / Pathak, S. / Schuttelkopf, A.W. / Borodkin, V. / Shepherd, S.M. / Ibrahim, A.F.M. / Van Aalten, D.M.F.
History
DepositionMay 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XCC0866
B: XCC0866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,17712
Polymers122,8492
Non-polymers1,32810
Water5,765320
1
A: XCC0866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1266
Polymers61,4251
Non-polymers7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: XCC0866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0516
Polymers61,4251
Non-polymers6265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)81.523, 100.096, 156.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.836491, -0.531158, -0.134738), (0.547658, -0.818774, -0.172278), (-0.018813, -0.217899, 0.97579)
Vector: -6.0761, -60.171, 25.8795)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein XCC0866


Mass: 61424.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8PC69

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Non-polymers , 5 types, 330 molecules

#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pr
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.59 Å3/Da / Density % sol: 52.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.921
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 70020 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4 / % possible all: 86.1

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.965 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1399 2 %RANDOM
Rwork0.193 ---
obs0.194 68619 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--4.43 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8324 0 58 320 8702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0218630
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.94811777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64151102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69422.392393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.216151247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9641584
X-RAY DIFFRACTIONr_chiral_restr0.110.21299
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216744
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_it0.7461.55471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35928687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.39233159
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.724.53085
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
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 103
Rwork0.212 4508
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)
12.7366-1.40430.72121.68930.47993.19560.26740.6421-0.3417-0.3334-0.2459-0.25430.47351.1374-0.02150.20520.18610.05710.29720.10470.1176-12.2543-64.541125.4731
22.63590.0442-0.38210.748-1.15992.92460.035-0.46080.04870.0777-0.0672-0.1097-0.13670.26880.0322-0.1271-0.0414-0.0302-0.10010.0298-0.1767-7.0752-34.058134.4114
31.43420.11390.53171.074-0.64442.42280.0192-0.25230.01070.00490.12090.2649-0.0791-0.2347-0.14-0.13280.0334-0.0016-0.0770.0781-0.104-35.8251-36.639529.9231
42.1752-0.41281.09890.9526-1.65052.9336-0.01550.52740.2301-0.22190.17060.28220.1645-1.039-0.15510.13630.1346-0.06570.5281-0.22240.24353.15047.4291.5718
52.22160.72940.10291.01440.44871.99960.0546-0.2858-0.02940.0687-0.02930.05430.0149-0.1606-0.0253-0.17660.0178-0.0048-0.21030.0152-0.203218.9151-21.912310.7324
61.00760.1703-0.22461.42950.09781.97760.0308-0.09990.3815-0.077-0.0218-0.1716-0.20350.15-0.009-0.1061-0.00770.0062-0.227-0.0444-0.014839.2387-1.77924.939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 163
2X-RAY DIFFRACTION2A164 - 359
3X-RAY DIFFRACTION2A542 - 567
4X-RAY DIFFRACTION3A360 - 541
5X-RAY DIFFRACTION4B21 - 163
6X-RAY DIFFRACTION5B164 - 359
7X-RAY DIFFRACTION5B542 - 567
8X-RAY DIFFRACTION6B360 - 541

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