[English] 日本語
Yorodumi
- PDB-1noh: The structure of bacteriophage phi29 scaffolding protein gp7 afte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1noh
TitleThe structure of bacteriophage phi29 scaffolding protein gp7 after prohead assembly
ComponentsHEAD MORPHOGENESIS PROTEIN
KeywordsVIRAL PROTEIN / coiled-coil
Function / homology
Function and homology information


viral scaffold / virion assembly / DNA binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #400 / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Capsid assembly scaffolding protein
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMorais, M.C. / Kanamaru, S. / Badasso, M.O. / Koti, J.S. / Owen, B.L. / McMurray, C.T. / L Anderson, D. / Rossmann, M.G.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Bacteriophage f29 scaffolding protein gp7 before and after prohead assembly
Authors: Morais, M.C. / Kanamaru, S. / Badasso, M.O. / Koti, J.S. / Owen, B.A.L. / McMurray, C.T. / Anderson, D.L. / Rossmann, M.G.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEAD MORPHOGENESIS PROTEIN
B: HEAD MORPHOGENESIS PROTEIN
C: HEAD MORPHOGENESIS PROTEIN
D: HEAD MORPHOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)44,6614
Polymers44,6614
Non-polymers00
Water0
1
A: HEAD MORPHOGENESIS PROTEIN
B: HEAD MORPHOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,3312
Polymers22,3312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-28 kcal/mol
Surface area9510 Å2
MethodPISA
2
C: HEAD MORPHOGENESIS PROTEIN
D: HEAD MORPHOGENESIS PROTEIN


Theoretical massNumber of molelcules
Total (without water)22,3312
Polymers22,3312
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-27 kcal/mol
Surface area9350 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-65 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.005, 117.301, 105.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221
DetailsThe biological unit is a dimeric coiled-coil. There are two such dimers per asymmetric unit.

-
Components

#1: Protein
HEAD MORPHOGENESIS PROTEIN / Bacteriophage phi29 scaffolding protein gp7 / LATE PROTEIN GP7 / gene 7 protein'


Mass: 11165.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Gene: gp7 / Plasmid: pARgp7 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P13848

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 76.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14.4 % Peg 8000, 0.08 M sodium cacodylate, 0.16 M calcium acetate, 20 % glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114.4 %(v/v)PEG800011
20.08 Msodium cacodylate11pH6.5
30.16 Mcadmium acetate11
420 %(v/v)glycerol11
51 mg/mlprotein11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→36.15 Å / Num. all: 27757 / Num. obs: 27757 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 33.1 Å2 / Rsym value: 0.091 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2.4 / Num. unique all: 1568 / Rsym value: 0.473 / % possible all: 95.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 17904 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.473

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NO4

1no4


Resolution: 2.8→36.15 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 2582 9.3 %RANDOM
Rwork0.254 ---
all0.258 27757 --
obs0.254 27757 82.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.9522 Å2 / ksol: 0.344448 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å20 Å2
2---11.24 Å20 Å2
3---14.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.84 Å
Refinement stepCycle: LAST / Resolution: 2.8→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 0 0 2356
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 368 10.1 %
Rwork0.402 3276 -
obs--65 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

+
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