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- PDB-2jlb: Xanthomonas campestris putative OGT (XCC0866), complex with UDP- ... -

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Basic information

Entry
Database: PDB / ID: 2jlb
TitleXanthomonas campestris putative OGT (XCC0866), complex with UDP- GlcNAc phosphonate analogue
ComponentsXCC0866
KeywordsTRANSFERASE / PROTEIN O-GLCNACYLATION / OGT / GT-B / TPR REPEAT / GLYCOSYL TRANSFERASE
Function / homology
Function and homology information


protein O-linked glycosylation / 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-UDM / O-GlcNAc transferase C-terminal domain-containing protein
Similarity search - Component
Biological speciesXANTHOMONAS CAMPESTRIS PV. CAMPESTRIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionSep 7, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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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)124,2057
Polymers122,8492
Non-polymers1,3565
Water2,684149
1
A: XCC0866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0853
Polymers61,4251
Non-polymers6602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: XCC0866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1204
Polymers61,4251
Non-polymers6963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.860, 100.527, 154.521
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:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUHISHISAA102 - 118102 - 118
21GLUGLUHISHISBB102 - 118102 - 118
12LEULEULEULEUAA131 - 144131 - 144
22LEULEULEULEUBB131 - 144131 - 144
13ALAALATHRTHRAA185 - 198185 - 198
23ALAALATHRTHRBB185 - 198185 - 198
14VALVALALAALAAA200 - 258200 - 258
24VALVALALAALABB200 - 258200 - 258
15PROPROTYRTYRAA305 - 342305 - 342
25PROPROTYRTYRBB305 - 342305 - 342
16GLYGLYARGARGAA351 - 368351 - 368
26GLYGLYARGARGBB351 - 368351 - 368
17GLYGLYLEULEUAA377 - 422377 - 422
27GLYGLYLEULEUBB377 - 422377 - 422
18PROPROVALVALAA440 - 533440 - 533
28PROPROVALVALBB440 - 533440 - 533
19ALAALAALAALAAA539 - 560539 - 560
29ALAALAALAALABB539 - 560539 - 560

NCS oper: (Code: given
Matrix: (-0.876299, 0.481721, -0.006676), (0.481718, 0.87593, -0.026352), (-0.006847, -0.026308, -0.99963)
Vector: 39.69, -9.649, 25.084)

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Components

#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
#2: Chemical ChemComp-UDM / URIDINE-DIPHOSPHATE-METHYLENE-N-ACETYL-GLUCOSAMINE / ((2S,3R,4R,5S,6R)-3-ACETAMIDO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YL)METHYLPHOSPHONIC (((2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHYL PHOSPHORIC) ANHYDRIDE


Mass: 605.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H29N3O16P2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.65 Å3/Da / Density % sol: 53.6 % / Description: NONE
Crystal growpH: 9 / Details: 83 MM CHES PH 9.0, 20.8% PEG 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 / Date: Feb 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 43895 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.73 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VSY

2vsy


Resolution: 2.5→19.83 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU B: 18.611 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.545 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 903 2.1 %RANDOM
Rwork0.21 ---
obs0.211 42804 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 81 149 8572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0218677
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.95911862
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30851096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50622.481391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.029151243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3121582
X-RAY DIFFRACTIONr_chiral_restr0.0880.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216773
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_it0.4761.55468
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94428679
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5333209
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.614.53183
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1288tight positional0.050.05
2B1288tight positional0.050.05
1A1147medium positional0.080.5
2B1147medium positional0.080.5
1A1288tight thermal0.080.5
2B1288tight thermal0.080.5
1A1147medium thermal0.12
2B1147medium thermal0.12
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 66
Rwork0.276 3067
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)
12.44020.03180.68450.84290.5315.6959-0.0105-0.5258-0.03650.1792-0.20820.42470.1085-1.58580.21870.1937-0.12670.06770.4519-0.09250.25435.0026-6.9968-1.2728
21.4601-0.19310.09181.04060.47530.79250.03570.08960.0535-0.0024-0.02740.05110.02-0.0861-0.0082-0.0773-0.02180.0008-0.08880.0305-0.100418.694221.42-10.7013
31.08530.1399-0.14011.0134-0.06521.5528-0.025-0.0085-0.12770.08770.0269-0.19150.19340.1051-0.0018-0.03220.0283-0.0326-0.0969-0.0059-0.046440.34363.1264-4.2515
41.741-0.4689-1.34040.66530.2951.63150.07960.11690.0241-0.1287-0.19560.04060.08990.09380.1160.08230.05270.0068-0.00190.0720.006732.023-13.380226.4962
51.17610.278-0.2170.8377-0.31161.258-0.0279-0.09590.06820.12760.0519-0.0202-0.07610.0761-0.0241-0.04-0.0106-0.0026-0.0676-0.003-0.061533.785418.48835.1121
61.7280.63950.24431.26650.2391.6876-0.06610.09070.1625-0.00930.14090.3901-0.1286-0.252-0.0748-0.07810.03450.00410.06430.10140.06515.845212.6428.9845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 163
2X-RAY DIFFRACTION2A164 - 359
3X-RAY DIFFRACTION2A542 - 567
4X-RAY DIFFRACTION3A360 - 541
5X-RAY DIFFRACTION4B21 - 163
6X-RAY DIFFRACTION5B164 - 359
7X-RAY DIFFRACTION5B542 - 568
8X-RAY DIFFRACTION6B360 - 541

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