[English] 日本語
Yorodumi
- PDB-6stt: Adenovirus 29 Fiber Knob protein in complex with Sialic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6stt
TitleAdenovirus 29 Fiber Knob protein in complex with Sialic acid
ComponentsFiber
KeywordsVIRAL PROTEIN / Adenovirus / Type 29 / Sialic Acid / 3D Structure / Fiber Knob
Function / homology
Function and homology information


adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell
Similarity search - Function
Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Fiber
Similarity search - Component
Biological speciesHuman adenovirus 29
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsBaker, A.T. / Mundy, R.M. / Rizkallah, P.J. / Parker, A.L.
CitationJournal: npj Viruses / Year: 2023
Title: Broad sialic acid usage amongst species D human adenovirus
Authors: Mundy, R.M. / Baker, A.T. / Bates, E.A. / Cunliffe, T.G. / Teijeira-Crespo, A. / Moses, E. / Rizkallah, P.J. / Parker, A.L.
History
DepositionSep 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.pdbx_database_id_DOI / _citation.year ..._citation.pdbx_database_id_DOI / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fiber
B: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6124
Polymers41,9932
Non-polymers6192
Water6,666370
1
A: Fiber
hetero molecules

A: Fiber
hetero molecules

A: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9186
Polymers62,9903
Non-polymers9283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area7840 Å2
ΔGint-37 kcal/mol
Surface area21400 Å2
MethodPISA
2
B: Fiber
hetero molecules

B: Fiber
hetero molecules

B: Fiber
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9186
Polymers62,9903
Non-polymers9283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_454-z-1,x,-y-11
crystal symmetry operation11_544y,-z-1,-x-11
Buried area7910 Å2
ΔGint-36 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.236, 104.236, 104.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

21B-658-

HOH

-
Components

#1: Protein Fiber


Mass: 20996.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human adenovirus 29 / Gene: L5 / Production host: Escherichia coli (E. coli) / References: UniProt: E1CIQ3
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M SPG Buffer, 25% PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.54→60.25 Å / Num. obs: 55982 / % possible obs: 100 % / Redundancy: 22.4 % / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.02 / Rrim(I) all: 0.096 / Net I/σ(I): 17.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.54-1.5722.32.376227627870.6050.5122.4251.4100
8.44-60.1818.70.03737839410.0070.0317799.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→60.25 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.971 / SU B: 3.999 / SU ML: 0.061 / SU R Cruickshank DPI: 0.0818 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 2767 4.9 %RANDOM
Rwork0.1398 ---
obs0.1423 53165 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.88 Å2 / Biso mean: 27.295 Å2 / Biso min: 15.28 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.54→60.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2852 0 42 370 3264
Biso mean--59.2 38.48 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132983
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172698
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.6494064
X-RAY DIFFRACTIONr_angle_other_deg1.4331.5766319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.815358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53325.524143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75515509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.171154
X-RAY DIFFRACTIONr_chiral_restr0.080.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023280
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
X-RAY DIFFRACTIONr_rigid_bond_restr4.36232983
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 206 -
Rwork0.263 3880 -
all-4086 -
obs--99.98 %
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)
12.3589-1.03040.48371.8114-0.35581.45270.05980.12450.217-0.1255-0.0916-0.3564-0.12730.01620.03180.03110.00770.03420.00780.01940.0761-19.1678-17.7965-37.8687
21.8015-1.00790.38722.3546-0.52231.4539-0.0928-0.12810.35350.10930.0656-0.2122-0.00940.12910.02720.0070.0082-0.01890.0319-0.03520.0753-17.783-19.174-66.3991
30.0035-0.0180.01080.9426-0.46480.23230.0042-0.0354-0.0087-0.2301-0.00410.01720.1362-0.0265-0.00010.3832-0.03120.03320.4573-0.03740.3029-33.5891-33.6237-52.0852
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A187 - 371
2X-RAY DIFFRACTION2B187 - 371
3X-RAY DIFFRACTION3A - B400 - 401

+
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://pdbjlvh1.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