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- PDB-3oy7: Crystal structure of a virus encoded glycosyltransferase in compl... -

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Basic information

Entry
Database: PDB / ID: 3oy7
TitleCrystal structure of a virus encoded glycosyltransferase in complex with GDP-mannose
ComponentsGlycosyltransferase B736L
KeywordsVIRAL PROTEIN / TRANSFERASE / Rossmann Fold / GLycosyltransferase / GDP-mannose / sugar / virus surface
Function / homologyRossmann fold - #11930 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE / Uncharacterized protein B736L
Function and homology information
Biological speciesParamecium bursaria Chlorella virus NY2A
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.73 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 23, 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _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: Glycosyltransferase B736L
B: Glycosyltransferase B736L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5694
Polymers93,3592
Non-polymers1,2112
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-32 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.248, 243.189, 67.402
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 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA1 - 1641 - 164
21METMETVALVALBB1 - 1641 - 164
12ASPASPTHRTHRAA165 - 372165 - 372
22ASPASPTHRTHRBB165 - 372165 - 372
13LYSLYSARGARGAA373 - 392373 - 392
23LYSLYSARGARGBB373 - 392373 - 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: Chemical ChemComp-GDD / GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE


Mass: 605.341 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O16P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: crystallization solution:100mM Tris-HCl pH7.0, 20% w/v PEG3350 soaking solution: 100mM Tris-HCl pH7.0, 20% w/v PEG3350, 10mM GDP-mannose , 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: 0.98 Å
DetectorType: MarCCD 300 / Detector: CCD / Date: Jan 1, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 34259 / Num. obs: 33711 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 19.1
Reflection shellResolution: 2.74→2.84 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.566 / % possible all: 86.7

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Processing

Software
NameClassification
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.73→130.19 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.888 / SU B: 35.939 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.688 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28965 1701 5 %RANDOM
Rwork0.25687 ---
obs0.25854 31999 98.69 %-
all-34259 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.923 Å2
Baniso -1Baniso -2Baniso -3
1-6.07 Å20 Å20 Å2
2---1.16 Å20 Å2
3----4.9 Å2
Refinement stepCycle: LAST / Resolution: 2.73→130.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 78 9 6289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226422
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.061.9618702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0475782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64323.586290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.406151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.321540
X-RAY DIFFRACTIONr_chiral_restr0.0720.2978
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024792
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_it0.221.53886
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41926294
X-RAY DIFFRACTIONr_scbond_it0.51132536
X-RAY DIFFRACTIONr_scangle_it0.8674.52408
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
11299medium positional0.30.5
21634medium positional0.340.5
3169medium positional0.290.5
11299medium thermal0.222
21634medium thermal0.242
3169medium thermal0.212
LS refinement shellResolution: 2.732→2.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 101 -
Rwork0.319 2085 -
obs--87.55 %
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)
14.4262-0.47741.59213.78310.58822.60520.31590.2004-0.2973-0.6351-0.2569-0.09610.3618-0.0437-0.05910.20150.08130.00150.24970.01070.3256-32.6352-65.5826-17.8573
25.2972-0.35212.51039.72651.95572.13010.4285-0.53661.3372-1.8914-1.49991.6717-0.8466-1.13741.07142.18190.619-0.37431.1016-0.33990.9693-31.3595-8.5434-18.7269
31.7473-1.0979-1.12853.08451.62724.24010.23990.22140.1436-0.4422-0.28270.0495-0.9641-0.06530.04280.2374-0.0225-0.0560.34660.06130.2891-16.4553-37.7295-13.909
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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