[English] 日本語
Yorodumi
- PDB-4dyc: Crystal Structure of the terminase small subunit gp1 with D19R mu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dyc
TitleCrystal Structure of the terminase small subunit gp1 with D19R mutation of the bacterial virus sf6
ComponentsTerminase small subunit
KeywordsVIRAL PROTEIN / gp1 / DNA-binding
Function / homologyHomeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Terminase small subunit
Function and homology information
Biological speciesSalmonella phage HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhao, H. / Tang, L.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Structural and Functional Studies of the Phage Sf6 Terminase Small Subunit Reveal a DNA-Spooling Device Facilitated by Structural Plasticity.
Authors: Zhao, H. / Kamau, Y.N. / Christensen, T.E. / Tang, L.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Terminase small subunit
B: Terminase small subunit


Theoretical massNumber of molelcules
Total (without water)31,1542
Polymers31,1542
Non-polymers00
Water3,693205
1
A: Terminase small subunit
B: Terminase small subunit

A: Terminase small subunit
B: Terminase small subunit

A: Terminase small subunit
B: Terminase small subunit

A: Terminase small subunit
B: Terminase small subunit


Theoretical massNumber of molelcules
Total (without water)124,6148
Polymers124,6148
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area32310 Å2
ΔGint-147 kcal/mol
Surface area44220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.570, 88.570, 73.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein Terminase small subunit


Mass: 15576.782 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage HK620 (virus) / Strain: bacteriophage Sf6 / Gene: gp1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLys / References: UniProt: Q9AZ01
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.4
Details: 1.2M NAH2PO4/0.8M K2HPO4, 0.2M LI2SO4, pH 6.4, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2010
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 27710 / Num. obs: 27608 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.57 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.61
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 13.03 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 4.45 / Num. unique all: 1938 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HEF

3hef


Resolution: 1.8→19.805 Å / SU ML: 0.02 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 4.45 / Phase error: 22.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1379 5 %Random
Rwork0.207 ---
obs0.2084 27574 99.64 %-
all-27710 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.089 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6427 Å20 Å20 Å2
2---3.6427 Å20 Å2
3---7.2854 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1973 0 0 205 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072011
X-RAY DIFFRACTIONf_angle_d0.9482710
X-RAY DIFFRACTIONf_dihedral_angle_d15.839763
X-RAY DIFFRACTIONf_chiral_restr0.068296
X-RAY DIFFRACTIONf_plane_restr0.004353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8003-1.86460.29911320.24532510X-RAY DIFFRACTION98
1.8646-1.93920.22221360.21042579X-RAY DIFFRACTION100
1.9392-2.02730.22891360.19662576X-RAY DIFFRACTION100
2.0273-2.13410.25221350.19532582X-RAY DIFFRACTION100
2.1341-2.26760.25271370.19822602X-RAY DIFFRACTION100
2.2676-2.44240.23691380.19482604X-RAY DIFFRACTION100
2.4424-2.68770.2531370.20752620X-RAY DIFFRACTION100
2.6877-3.07530.22411390.2072638X-RAY DIFFRACTION100
3.0753-3.86990.22431410.20012666X-RAY DIFFRACTION100
3.8699-19.8060.22811480.2112818X-RAY DIFFRACTION100

+
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