[English] 日本語
Yorodumi
- PDB-8asa: Crystal structure of AO75L -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8asa
TitleCrystal structure of AO75L
ComponentsExostosin
KeywordsTRANSFERASE / Glycosyltransferase / PBCV-1 / Xylosyltransferase / Glycans / VIRAL PROTEIN
Function / homologyExostosin GT47 domain-containing protein
Function and homology information
Biological speciesParamecium bursaria Chlorella virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLaugeri, M.E. / Speciale, I. / Gimeno, A. / Lin, S. / Poveda, A. / Lowary, T. / Van Etten, J.L. / Barbero, J.J. / De Castro, C. / Tonetti, M. / Rojas, A.L.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesSEV20160644 Spain
CitationJournal: To Be Published
Title: Crystal structure of AO75L
Authors: Laugeri, M.E. / Speciale, I. / Gimeno, A. / Lin, S. / Poveda, A. / Lowary, T. / Van Etten, J.L. / Barbero, J.J. / De Castro, C. / Tonetti, M. / Rojas, A.L.
History
DepositionAug 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exostosin
B: Exostosin
C: Exostosin
D: Exostosin
E: Exostosin
F: Exostosin
G: Exostosin
H: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,812112
Polymers271,5438
Non-polymers6,270104
Water20,5911143
1
A: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,94918
Polymers33,9431
Non-polymers1,00617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,76214
Polymers33,9431
Non-polymers81913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,75112
Polymers33,9431
Non-polymers80811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,13622
Polymers33,9431
Non-polymers1,19321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,52512
Polymers33,9431
Non-polymers58311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,59912
Polymers33,9431
Non-polymers65711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,60813
Polymers33,9431
Non-polymers66512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Exostosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4839
Polymers33,9431
Non-polymers5408
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.708, 90.772, 91.676
Angle α, β, γ (deg.)90.460, 108.600, 109.710
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Exostosin / A075L


Mass: 33942.836 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Gene: A075L / Production host: Escherichia coli (E. coli) / References: UniProt: Q89410

-
Non-polymers , 6 types, 1247 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1143 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8.1
Details: 37.5% PEG3350, PEG1K, MPD 0.1M Tris-0.1M Bicine 0.03M MgCl2, 0.03CaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.919319 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2020
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919319 Å / Relative weight: 1
ReflectionResolution: 2.18→76.84 Å / Num. obs: 237952 / % possible obs: 92.1 % / Redundancy: 1.796 % / Biso Wilson estimate: 43.193 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.076 / Χ2: 0.925 / Net I/σ(I): 9.84 / Num. measured all: 427470
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.18-2.311.7760.3732.366376141722359090.7730.52786.1
2.31-2.471.8250.2623.426827439378374030.8580.37195
2.47-2.671.7680.1794.746109036498345590.9220.25294.7
2.67-2.921.7890.1087.185651233624315870.9690.15393.9
2.92-3.271.8410.06411.25221030348283550.9880.09193.4
3.27-3.771.7560.04216.064364926902248620.9940.05992.4
3.77-4.621.8370.03221.693813022602207570.9950.04591.8
4.62-6.521.7730.0322.172786117560157150.9960.04389.5
6.52-76.841.8150.02425.2715983965888050.9970.03491.2

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→76.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.273 / SU ML: 0.179 / SU R Cruickshank DPI: 0.3371 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 6319 5.2 %RANDOM
Rwork0.1938 ---
obs0.1962 115844 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.51 Å2 / Biso mean: 39.389 Å2 / Biso min: 14.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20.04 Å20.4 Å2
2--0.89 Å2-0.26 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.2→76.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18778 0 354 1143 20275
Biso mean--53.33 42.9 -
Num. residues----2245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01319602
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718076
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.65226455
X-RAY DIFFRACTIONr_angle_other_deg1.1131.57942036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73752262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.8322.9061115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.306153394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.84315114
X-RAY DIFFRACTIONr_chiral_restr0.0510.22541
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0221370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024196
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 465 -
Rwork0.253 8500 -
all-8965 -
obs--96.42 %

+
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