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- PDB-3oy2: Crystal structure of a putative glycosyltransferase from Parameci... -

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Basic information

Entry
Database: PDB / ID: 3oy2
TitleCrystal structure of a putative glycosyltransferase from Paramecium bursaria Chlorella virus NY2A
ComponentsGlycosyltransferase B736L
KeywordsVIRAL PROTEIN / TRANSFERASE / Rossmann fold / glycosyltransferase / GDP-mannose / sugar / Virus capsid proteins
Function / homologyRossmann fold - #11930 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein B736L
Function and homology information
Biological speciesParamecium bursaria Chlorella virus NY2A
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsXiang, Y. / Rossmann, M.G.
CitationJournal: J.Virol. / Year: 2010
Title: Crystal structure of a virus-encoded putative glycosyltransferase
Authors: Xiang, Y. / Baxa, U. / Zhang, Y. / Steven, A.C. / Lewis, G.L. / Van Etten, J.L. / Rossmann, M.G.
History
DepositionSep 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyltransferase B736L
B: Glycosyltransferase B736L


Theoretical massNumber of molelcules
Total (without water)93,3592
Polymers93,3592
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-11 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.615, 246.941, 67.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYS4AA165 - 373165 - 373
21ASPASPLYSLYS4BB165 - 373165 - 373
12METMETVALVAL3AA1 - 1641 - 164
22METMETVALVAL3BB1 - 1641 - 164
13PROPROARGARG4AA374 - 392374 - 392
23PROPROARGARG4BB374 - 392374 - 392

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Glycosyltransferase B736L


Mass: 46679.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus NY2A
Gene: B736L, NY2A_B736L / Production host: Escherichia coli (E. coli) / References: UniProt: A7IXR1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris-HCl pH7.0, 20% w/v PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: MarCCD 300 / Detector: CCD / Date: Jan 1, 2008
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 56157 / Num. obs: 56045 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.074 / Rsym value: 0.074
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.31→130.19 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.129 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.217
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 2843 5.1 %RANDOM
Rwork0.233 ---
obs0.23476 53234 99.35 %-
all-56157 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.933 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2---0.17 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.31→130.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 0 107 6309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.9428572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9345782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.3723.586290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.176151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2121540
X-RAY DIFFRACTIONr_chiral_restr0.1520.2956
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214768
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_it0.6241.53886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19226294
X-RAY DIFFRACTIONr_scbond_it1.97132452
X-RAY DIFFRACTIONr_scangle_it2.9854.52278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
2656tight positional0.050.05
11643medium positional0.40.5
3160medium positional0.330.5
2643loose positional0.065
2656tight thermal0.140.5
11643medium thermal1.082
3160medium thermal0.752
2643loose thermal0.210
LS refinement shellResolution: 2.311→2.371 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 204 -
Rwork0.295 3558 -
obs--91.78 %
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)
12.89581.27191.68381.75140.92952.48540.06830.1365-0.3557-0.08190.0322-0.02530.28870.1306-0.10050.1511-0.0268-0.01230.1844-0.020.3062-32.5001-66.2523-17.6425
21.1192-0.12150.90358.2242.73665.06250.0223-0.00370.5177-1.0245-0.78851.428-1.6481-1.23580.76621.4420.3105-0.25620.5886-0.11660.7396-31.5908-8.7671-18.2983
31.0612-0.0442-0.43661.38260.52523.76910.06660.07170.0973-0.2443-0.08020.1588-0.83010.21850.01360.2213-0.11-0.04610.25650.02140.2146-16.6324-37.8979-13.6403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 163
2X-RAY DIFFRACTION2B1 - 163
3X-RAY DIFFRACTION3A164 - 392
4X-RAY DIFFRACTION3B164 - 392

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