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- PDB-2p6w: Crystal structure of a glycosyltransferase involved in the glycos... -

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Basic information

Entry
Database: PDB / ID: 2p6w
TitleCrystal structure of a glycosyltransferase involved in the glycosylation of the major capsid of PBCV-1
ComponentsPutative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein
KeywordsTRANSFERASE / glycosyltransferase / PBCV
Function / homology
Function and homology information


glycosyltransferase activity / nucleotide binding / membrane / metal ion binding
Similarity search - Function
Glycosyltransferase 34 / galactosyl transferase GMA12/MNN10 family / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / : / UDP-Glucose glycosyltransferase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsZhang, Y. / Ye, X. / Van Etten, J.L. / Rossmann, M.G.
CitationJournal: Structure / Year: 2007
Title: Structure and function of a chlorella virus-encoded glycosyltransferase.
Authors: Zhang, Y. / Xiang, Y. / Van Etten, J.L. / Rossmann, M.G.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.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.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_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: Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4063
Polymers25,1621
Non-polymers2442
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.229, 63.017, 44.772
Angle α, β, γ (deg.)90.00, 115.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein / Vp54


Mass: 25162.436 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Gene: A64R / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q89399
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM socium citrate, 200mM NaCl, 25% PEG3500, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection

D res high: 2 Å / D res low: 40 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2Num. obs% possible obs
7115.11034160.0722.161477899.6
7216.61029520.0752.831462599.6
7.2312.31058580.0852.321479499.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.314010010.0492.7827.5
3.424.3110010.0532.7317.7
2.993.4210010.0682.7347.7
2.712.9910010.0832.2557.7
2.522.7110010.0861.7437.7
2.372.5210010.11.6467.7
2.252.3710010.1171.8567.5
2.152.2510010.1342.1176.4
2.072.1599.910.1511.6545.6
22.0796.110.1591.6894.5
4.314010020.0594.8017.5
3.424.3110020.0593.7487.7
2.993.4210020.0713.4467.7
2.712.9910020.0863.2167.7
2.522.7110020.0862.2587.7
2.372.5210020.0931.9757.7
2.252.3710020.1061.9697.5
2.152.2510020.1212.4016.5
2.072.1599.920.1291.8295.7
22.0796.420.1351.7574.7
4.314099.930.0533.1457.5
3.424.3110030.0593.6257.7
2.993.4210030.0772.6577.7
2.712.9910030.0992.7597.7
2.522.7110030.1121.8497.7
2.372.5210030.1311.7147.7
2.252.3710030.1511.6427.6
2.152.2599.930.181.9777.1
2.072.1599.230.1991.6575.9
22.0797.930.2251.6715.1
ReflectionResolution: 1.5→30 Å / Num. obs: 31588 / % possible obs: 90.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.067 / Χ2: 2.542 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.551.70.42912562.202136.2
1.55-1.622.10.35825442.023173.7
1.62-1.693.20.34833852.158197.9
1.69-1.783.50.28134422.214198.9
1.78-1.893.50.19634642.3199.4
1.89-2.043.50.14334812.62199.6
2.04-2.243.60.10234692.804199.8
2.24-2.563.60.07934862.932199.9
2.56-3.233.70.05934953.007199.9
3.23-303.70.03635662.4199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
SHARPphasing
RefinementResolution: 1.6→8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.079 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2812 10 %RANDOM
Rwork0.172 ---
obs0.175 28206 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.577 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å21.44 Å2
2---0.73 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 14 164 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221809
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9342465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00323.76393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8615289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.859158
X-RAY DIFFRACTIONr_chiral_restr0.2310.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021415
X-RAY DIFFRACTIONr_nbd_refined0.2010.2880
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.27
X-RAY DIFFRACTIONr_mcbond_it0.7211.51072
X-RAY DIFFRACTIONr_mcangle_it1.06621705
X-RAY DIFFRACTIONr_scbond_it1.7833866
X-RAY DIFFRACTIONr_scangle_it2.5574.5760
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 188 -
Rwork0.225 1703 -
obs-1891 94.46 %
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)
10.2594-0.0506-0.06790.2922-0.07780.2607-0.00420.0089-0.00590.0246-0.0098-0.0023-0.0013-0.01420.0141-0.0126-0.0039-0.0016-0.0092-0.0072-0.014632.097612.81835.4062
23.10541.8775-8.81982.6331.111552.7705-0.06620.26890.4957-0.92220.4294-0.28870.7375-0.1009-0.3632-0.0058-0.010.0008-0.00430.0129-0.012230.2554.8056-0.5498
3000000000000000-0.0096-0.005-0.00960.00730.00950.008730.75055.69812.287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 208
2X-RAY DIFFRACTION2A802
3X-RAY DIFFRACTION3A214

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