[English] 日本語
Yorodumi
- PDB-6orj: Central spike of phiKZ phage tail -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6orj
TitleCentral spike of phiKZ phage tail
ComponentsPHIKZ164
KeywordsVIRAL PROTEIN / Membrane puncturing device / beta-helix / OB-fold / trimer / VgrG-like
Function / homologyPHIKZ164
Function and homology information
Biological speciesPseudomonas virus phiKZ
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.37 Å
AuthorsLeiman, P.G. / Browning, C. / Shneider, M.M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To Be Published
Title: Central spike of phiKZ phage tail
Authors: Leiman, P.G. / Browning, C. / Shneider, M.M.
History
DepositionApr 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHIKZ164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,21110
Polymers32,9031
Non-polymers3089
Water3,999222
1
A: PHIKZ164
hetero molecules

A: PHIKZ164
hetero molecules

A: PHIKZ164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,63430
Polymers98,7093
Non-polymers92527
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area29030 Å2
ΔGint-331 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.595, 82.595, 345.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-307-

NA

-
Components

#1: Protein PHIKZ164


Mass: 32903.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas virus phiKZ / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: Q8SCZ8
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 5.18 Å3/Da / Density % sol: 76.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 4 M sodium chloride, 100 mM CHES, pH 9.0, 0.3% w/v sorbitol or adonitol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Type: SLS BEAMLINE X06DA / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 22, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 51342 / % possible obs: 95.1 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.086 / Net I/σ(I): 22.92
Reflection shellResolution: 2.37→2.51 Å / Redundancy: 5.65 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 6654 / Rrim(I) all: 0.89 / % possible all: 76.1

-
Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.37→44.889 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 2560 5 %random
Rwork0.1753 ---
obs0.1768 51247 95.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.7 Å2
Refinement stepCycle: LAST / Resolution: 2.37→44.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 12 222 2144
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)
15.2029-0.1704-0.84264.52230.23255.03630.01910.6853-0.1733-0.4615-0.14030.48590.1155-0.50490.05260.2589-0.0158-0.08510.2719-0.0270.282427.795722.4522-11.3192
22.9459-0.70741.38811.8628-1.35484.9685-0.02460.24160.1267-0.1298-0.03720.03450.0094-0.0880.07780.1574-0.0224-0.01580.1954-0.02750.240630.600223.2911-3.7636
34.6268-5.0829-5.68866.69756.62898.0446-0.03430.7477-0.8181-0.7151-0.54411.8089-0.3671-1.51130.57120.4273-0.0116-0.04210.3981-0.02870.599736.63054.91310.2161
40.37850.01380.3280.47760.20873.6890.0165-0.2503-0.02530.2304-0.0380.03140.2223-0.15620.03290.3102-0.01550.02470.32380.00710.220337.4220.200744.5934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 97 )A21 - 97
2X-RAY DIFFRACTION2chain 'A' and (resid 98 through 145 )A98 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 159 )A146 - 159
4X-RAY DIFFRACTION4chain 'A' and (resid 160 through 298 )A160 - 298

+
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