[English] 日本語
Yorodumi
- PDB-2p72: crystal structure of a glycosyltransferase involved in the glycos... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.41 %

-
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

-
Phasing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more