[English] 日本語
Yorodumi
- PDB-1x35: Recombinant T=3 capsid of a site specific mutant of SeMV CP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x35
TitleRecombinant T=3 capsid of a site specific mutant of SeMV CP
ComponentsCoat protein
KeywordsVIRUS / T=3 capsids / beta-annulus / Icosahedral virus
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / metal ion binding / Capsid protein
Function and homology information
Biological speciesSesbania mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsSangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Saravanan, V. / Vijay, C.S. / Savithri, H.S. / Murthy, M.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structural studies on recombinant T = 3 capsids of Sesbania mosaic virus coat protein mutants.
Authors: Sangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Saravanan, V. / Vijay, C.S. / Savithri, H.S. / Murthy, M.R.
History
DepositionApr 29, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _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_asym_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_asym_id / _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_asym_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
Revision 1.4Nov 13, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0966
Polymers85,9763
Non-polymers1203
Water00
1
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,165,768360
Polymers5,158,554180
Non-polymers7,214180
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 5


  • icosahedral pentamer
  • 430 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)430,48130
Polymers429,87915
Non-polymers60115
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 517 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)516,57736
Polymers515,85518
Non-polymers72118
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: Coat protein
B: Coat protein
C: Coat protein
hetero molecules
x 30


  • crystal asymmetric unit, crystal frame
  • 2.58 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,582,884180
Polymers2,579,27790
Non-polymers3,60790
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)471.500, 330.095, 351.474
Angle α, β, γ (deg.)90.00, 131.05, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)149.27166, 56.43043, -34.87592
3generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)258.49027, -46.89492, 28.98265
4generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)176.71943, -167.18392, 103.32534
5generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)16.96366, -138.20127, 85.41308
6generate(-1), (-1), (1)240.57801
7generate(-0.30901699, -0.80901699, 0.5), (0.80901699, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699)91.30635, -56.43043, -34.87592
8generate(0.80901699, -0.5, 0.30901699), (0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5)-17.91226, 46.89492, 28.98265
9generate(0.80901699, 0.5, -0.30901699), (-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5)63.85858, 167.18392, 103.32534
10generate(-0.30901699, 0.80901699, -0.5), (-0.80901699, -0.5, -0.30901699), (-0.5, 0.30901699, 0.80901699)223.61435, 138.20127, 85.41308
11generate(-1), (-1), (1)252.597, 120.289, 132.308
12generate(-0.5, -0.30901699, -0.80901699), (-0.30901699, -0.80901699, 0.5), (-0.80901699, 0.5, 0.30901699)287.47292, -28.98265, 188.73843
13generate(-0.30901699, -0.80901699, -0.5), (0.80901699, -0.5, 0.30901699), (-0.5, -0.30901699, 0.80901699)223.61435, -138.20127, 85.41308
14generate(0.30901699, -0.80901699, -0.5), (0.80901699, 0.5, -0.30901699), (0.5, -0.30901699, 0.80901699)149.27166, -56.43043, -34.87592
15generate(0.5, -0.30901699, -0.80901699), (-0.30901699, 0.80901699, -0.5), (0.80901699, 0.5, 0.30901699)167.18392, 103.32534, -5.89327
16generate(-1), (1), (-1)252.597, -120.289, 132.308
17generate(-0.5, -0.30901699, -0.80901699), (0.30901699, 0.80901699, -0.5), (0.80901699, -0.5, -0.30901699)287.47292, 28.98265, 75.87757
18generate(-0.30901699, -0.80901699, -0.5), (-0.80901699, 0.5, -0.30901699), (0.5, 0.30901699, -0.80901699)223.61435, 138.20127, 179.20291
19generate(0.30901699, -0.80901699, -0.5), (-0.80901699, -0.5, 0.30901699), (-0.5, 0.30901699, -0.80901699)149.27166, 56.43043, 299.49192
20generate(0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5), (-0.80901699, -0.5, -0.30901699)167.18392, -103.32534, 270.50926
21generate(-1), (1), (-1)120.289, -132.308, 252.597
22generate(0.80901699, -0.5, -0.30901699), (0.5, 0.30901699, 0.80901699), (-0.30901699, -0.80901699, 0.5)63.85858, -167.18392, 103.32534
23generate(0.5, 0.30901699, -0.80901699), (0.30901699, 0.80901699, 0.5), (0.80901699, -0.5, 0.30901699)167.18392, -103.32534, -5.89327
24generate(-0.5, 0.30901699, -0.80901699), (-0.30901699, 0.80901699, 0.5), (0.80901699, 0.5, -0.30901699)287.47292, -28.98265, 75.87757
25generate(-0.80901699, -0.5, -0.30901699), (-0.5, 0.30901699, 0.80901699), (-0.30901699, 0.80901699, -0.5)258.49027, -46.89492, 235.63334
26generate(-1), (-1), (1)120.289, 132.308, 12.01899
27generate(0.80901699, -0.5, -0.30901699), (-0.5, -0.30901699, -0.80901699), (0.30901699, 0.80901699, -0.5)63.85858, 167.18392, 161.29065
28generate(0.5, 0.30901699, -0.80901699), (-0.30901699, -0.80901699, -0.5), (-0.80901699, 0.5, -0.30901699)167.18392, 103.32534, 270.50926
29generate(-0.5, 0.30901699, -0.80901699), (0.30901699, -0.80901699, -0.5), (-0.80901699, -0.5, 0.30901699)287.47292, 28.98265, 188.73843
30generate(-0.80901699, -0.5, -0.30901699), (0.5, -0.30901699, -0.80901699), (0.30901699, -0.80901699, 0.5)258.49027, 46.89492, 28.98265

-
Components

#1: Protein Coat protein


Mass: 28658.633 Da / Num. of mol.: 3 / Mutation: P53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EB06
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 6% PEG 3350, 0.1M MgCl2, Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 2004
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 4.1→20 Å / Num. all: 352930 / Num. obs: 324695 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 4.1→4.25 Å / % possible all: 74.8

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 29326465.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 14626 4.9 %RANDOM
Rwork0.268 ---
all0.268 301529 --
obs-297206 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.492238 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å20 Å27.2 Å2
2---2.66 Å20 Å2
3---4.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.55 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 4.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4439 0 3 0 4442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg2.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d3.32
X-RAY DIFFRACTIONc_mcbond_it11.61.5
X-RAY DIFFRACTIONc_mcangle_it17.992
X-RAY DIFFRACTIONc_scbond_it25.62
X-RAY DIFFRACTIONc_scangle_it33.242.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 4.1→4.35 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 2264 4.9 %
Rwork0.302 44141 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top

+
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