[English] 日本語
Yorodumi
- PDB-2oh6: The Crystal Structure of Recombinant Cypovirus Polyhedra -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oh6
TitleThe Crystal Structure of Recombinant Cypovirus Polyhedra
ComponentsPolyhedrin
KeywordsStructural Protein / RNA binding protein / beta sandwich / intracellular crystal / nucleotide binding
Function / homologyCypovirus polyhedrin, Cypovirus 1 type / Cypovirus polyhedrin protein / GTP binding / ATP binding / identical protein binding / ADENOSINE-5'-TRIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Polyhedrin
Function and homology information
Biological speciesBombyx mori cypovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsCoulibaly, F. / Chiu, E. / Ikeda, K. / Gutmann, S. / Haebel, P.W. / Schulze-Briese, C. / Mori, H. / Metcalf, P.
CitationJournal: Nature / Year: 2007
Title: The molecular organization of cypovirus polyhedra.
Authors: Coulibaly, F. / Chiu, E. / Ikeda, K. / Gutmann, S. / Haebel, P.W. / Schulze-Briese, C. / Mori, H. / Metcalf, P.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 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_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyhedrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9587
Polymers28,3601
Non-polymers1,5986
Water2,558142
1
A: Polyhedrin
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)359,49584
Polymers340,32412
Non-polymers19,17172
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation10_656-y+1,z,-x+11
Unit cell
Length a, b, c (Å)102.955, 102.955, 102.955
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
DetailsThe whole micron-sized crystals, called polyhedra, are the biological units. Polyhedra crystallize in the cytoplasm of CPV-infected insect cells and protect the virus particles.

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Polyhedrin / / C-polyhedrin


Mass: 28360.355 Da / Num. of mol.: 1 / Mutation: N29S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori cypovirus 1 / Species: Cypovirus 1 / Strain: CPV1 / Gene: Polyhedrin / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 (IPLB-SF21AE) / References: UniProt: O10693

-
Non-polymers , 6 types, 148 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal growTemperature: 300 K
Details: The crystals used to determine this structure were directly purified from cells, in vivo crystallization in the cytoplasm of the cell, temperature 300K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97885 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 3, 2005 / Details: MD2 diffractometer
RadiationMonochromator: sagittally horizontal focussing Si(111); meridionally vertical focussing Rh-coated mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97885 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. all: 10773 / Num. obs: 10547 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.132 / Χ2: 1.06 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1045 / Χ2: 1.014 / % possible all: 98.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→14.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.671 / SU ML: 0.124 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.626 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1037 9.9 %RANDOM
Rwork0.129 ---
all0.135 10697 --
obs0.135 10471 97.89 %-
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: 15.523 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 95 142 2244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212157
X-RAY DIFFRACTIONr_bond_other_d0.0020.021412
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9832946
X-RAY DIFFRACTIONr_angle_other_deg0.8373.0013397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5755246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14223.805113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3311514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02454
X-RAY DIFFRACTIONr_nbd_refined0.2060.2416
X-RAY DIFFRACTIONr_nbd_other0.1910.21477
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21042
X-RAY DIFFRACTIONr_nbtor_other0.0840.21115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2130
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.255
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.2190
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.259
X-RAY DIFFRACTIONr_mcbond_it0.8321.51591
X-RAY DIFFRACTIONr_mcbond_other0.1521.5500
X-RAY DIFFRACTIONr_mcangle_it1.06821982
X-RAY DIFFRACTIONr_scbond_it1.85831129
X-RAY DIFFRACTIONr_scangle_it2.7174.5964
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 53 -
Rwork0.166 680 -
obs-733 97.99 %

+
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