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- PDB-2p72: crystal structure of a glycosyltransferase involved in the glycos... -

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Basic information

Entry
Database: PDB / ID: 2p72
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-1
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
: / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-Glucose glycosyltransferase
Similarity search - Component
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Y. / Xiang, Y. / 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
B: Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0015
Polymers50,3252
Non-polymers6763
Water2,486138
1
A: Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2172
Polymers25,1621
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative glycosyltransferase (Mannosyltransferase) involved in glycosylating the PBCV-1 major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7843
Polymers25,1621
Non-polymers6212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.448, 61.776, 76.091
Angle α, β, γ (deg.)90.00, 126.56, 90.00
Int Tables number5
Space group name H-MC121

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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.: 2 / Fragment: N-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Genus: Chlorovirus / Gene: A64R / Plasmid: PTYB-1 / 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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.43 Å3/Da / Density % sol: 49.41 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 32704 / % possible obs: 94.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Χ2: 3.053 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.023.40.45631752.12192.8
2.02-2.13.40.33831672.314193.2
2.1-2.23.40.26532312.391193.4
2.2-2.313.40.20232112.552194.5
2.31-2.463.40.15332832.894194.7
2.46-2.653.40.11932593.146195.2
2.65-2.913.30.08932983.41196
2.91-3.333.20.06433443.706196.7
3.33-4.1930.04933414.125196.2
4.19-2030.04433954.124195.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.14 Å19.66 Å
Translation2.14 Å19.66 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 9.851 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1549 5.1 %RANDOM
Rwork0.207 ---
obs0.208 30485 96.09 %-
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: 44.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20.12 Å2
2--0.2 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 38 138 3555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223537
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9384824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79523.483178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15915551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8481516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022731
X-RAY DIFFRACTIONr_nbd_refined0.1920.21621
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22361
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.29
X-RAY DIFFRACTIONr_mcbond_it0.7181.52102
X-RAY DIFFRACTIONr_mcangle_it1.06923311
X-RAY DIFFRACTIONr_scbond_it1.79531712
X-RAY DIFFRACTIONr_scangle_it2.4794.51513
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 112 -
Rwork0.243 1988 -
obs-2100 93.29 %
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)
11.49530.7558-0.17073.1208-1.41.4519-0.07390.10550.0191-0.48280.23930.23790.2728-0.1192-0.16540.2036-0.03540.0083-0.21490.0206-0.1647-0.081-0.16922.372
21.8567-0.10960.24732.64480.93572.67830.00990.02850.09680.680.1918-0.08950.55980.2288-0.20180.28130.09620.0022-0.2943-0.0123-0.1885-19.41425.459-0.062
358.164-19.4788-17.275612.60388.19499.8483-0.1542-0.8457-0.840.284-0.21840.0533-0.5550.03490.37260.24780.08620.0252-0.1305-0.0054-0.2457-19.66231.757-7.483
46.53822.7455-5.10511.1783-1.684812.2582-0.1654-0.1022-0.97750.0292-0.7193.38091.74830.75920.88440.57110.10280.1946-0.16620.0677-0.34041.501-8.06920.363
51.4853-1.1774-0.39024.42321.3010.99610.0260.2637-0.0444-0.88070.1024-1.3251-0.2327-0.3489-0.12840.25570.04530.135-0.129-0.0008-0.0509-19.5832.65-3.065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 206
2X-RAY DIFFRACTION2B4 - 208
3X-RAY DIFFRACTION3B215
4X-RAY DIFFRACTION4A214
5X-RAY DIFFRACTION5B214

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