[English] 日本語
Yorodumi
- PDB-3zmo: VP16, a capsid protein of bacteriophage P23-77 (VP16-type-1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zmo
TitleVP16, a capsid protein of bacteriophage P23-77 (VP16-type-1)
ComponentsVP16
KeywordsVIRAL PROTEIN
Function / homologyJelly Rolls - #1180 / Jelly Rolls / Sandwich / Mainly Beta / identical protein binding / DI(HYDROXYETHYL)ETHER / VP16
Function and homology information
Biological speciesTHERMUS PHAGE P23-77 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsRissanen, I. / Grimes, J.M. / Pawlowski, A. / Mantynen, S. / Harlos, K. / Bamford, J.K.H. / Stuart, D.I.
CitationJournal: Structure / Year: 2013
Title: Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of an Ancient Branch from a Major Virus Lineage.
Authors: Rissanen, I. / Grimes, J.M. / Pawlowski, A. / Mantynen, S. / Harlos, K. / Bamford, J.K.H. / Stuart, D.I.
History
DepositionFeb 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_special_symmetry / Item: _exptl_crystal_grow.method
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5287
Polymers19,1281
Non-polymers4006
Water3,819212
1
A: VP16
hetero molecules

A: VP16
hetero molecules

A: VP16
hetero molecules

A: VP16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,11028
Polymers76,5114
Non-polymers1,59924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_755-x+y+2,y,-z1
crystal symmetry operation4_755-x+2,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area17140 Å2
ΔGint-68.9 kcal/mol
Surface area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.850, 61.850, 251.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1175-

NA

21A-1176-

NA

31A-1177-

PEG

-
Components

#1: Protein VP16


Mass: 19127.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SUBUNIT OF A STRAND-SWAPPED HOMODIMER / Source: (gene. exp.) THERMUS PHAGE P23-77 (virus) / Plasmid: PIR2 (ORF16/PET22B) / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): HMS174(DE3) / References: UniProt: C8CHL4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 3.63 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.4
Details: SITTING DROP VAPOUR DIFFUSION SYSTEM, MICROLITER DROPS OF PROTEIN (2-3 MG/ML IN 20 MM TRIS-BUFFER PH 7.4) MIXED 1:1 WITH A SOLUTION CONSISTING 5%(W/V) PEG1000 AND 5%(W/V) PEG8000 (DISSOLVED IN AUTOCLAVED WATER).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→62.8 Å / Num. obs: 27581 / % possible obs: 100 % / Redundancy: 28.5 % / Biso Wilson estimate: 33.08 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 30.7
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 21 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 3.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
ARP/wARPmodel building
XDSdata reduction
xia2data scaling
xia2phasing
SHELXDphasing
autoSHARPphasing
ARP/wARPphasing
BUSTER2.11.2refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.8→53.56 Å / Cor.coef. Fo:Fc: 0.9546 / Cor.coef. Fo:Fc free: 0.9298 / SU R Cruickshank DPI: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.103 / SU Rfree Blow DPI: 0.1 / SU Rfree Cruickshank DPI: 0.093 / Details: RESIDUE 1 IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 1383 5.03 %RANDOM
Rwork0.1885 ---
obs0.1898 27503 99.62 %-
Displacement parametersBiso mean: 44.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.7265 Å20 Å20 Å2
2--0.7265 Å20 Å2
3----1.4529 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 1.8→53.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1345 0 24 212 1581
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011433HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.031977HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d480SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes201HARMONIC5
X-RAY DIFFRACTIONt_it1433HARMONIC10
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion15.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion178SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1706SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.87 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2279 147 5.37 %
Rwork0.206 2591 -
all0.2071 2738 -
obs--99.62 %
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)
10.2828-0.20460.6883-0.1157-0.81560.1534-0.01660.0014-0.00490.03230.0097-0.02050.0390.02530.0069-0.04210.1044-0.00150.17270.1746-0.08881.7602-15.120634.7436
22.1875-0.47320.08370.3118-0.13443.2299-0.0294-0.0081-0.03550.059-0.1208-0.0345-0.0144-0.28260.1501-0.1749-0.0192-0.00410.0508-0.0134-0.056555.61170.758816.8908
31.1125-0.3294-1.18111.50190.69522.9363-0.07210.07360.02420.09530.0041-0.0069-0.1021-0.33050.0679-0.15240.0090.0060.1247-0.0215-0.063950.40383.789819.6123
42.2249-0.8871-2.762-0.98350.99073.2774-0.00270.0233-0.0470.038-0.077-0.00860.0186-0.11920.0797-0.1567-0.0312-0.01410.2303-0.114-0.071842.25542.541626.3701
50.3853-0.2928-0.3711.38151.0422.1648-0.02050.00150.06120.1121-0.0167-0.0921-0.2792-0.17290.0372-0.07970.0659-0.0350.1216-0.0432-0.032851.71210.618521.3906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 2-16
2X-RAY DIFFRACTION2CHAIN A AND RESID 17-78
3X-RAY DIFFRACTION3CHAIN A AND RESID 79-105
4X-RAY DIFFRACTION4CHAIN A AND RESID 106-126
5X-RAY DIFFRACTION5CHAIN A AND RESID 127-173

+
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