[English] 日本語
Yorodumi
- PDB-3sbb: Disulphide-mediated Tetramer of T4 Lysozyme R76C/R80C by Syntheti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sbb
TitleDisulphide-mediated Tetramer of T4 Lysozyme R76C/R80C by Synthetic Symmetrization
ComponentsLysozyme
KeywordsHYDROLASE / metal-mediated synthetic symmetrization / synthetic symmetrization
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.434 Å
AuthorsLaganowsky, A. / Soriaga, A.B. / Zhao, M. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2011
Title: An approach to crystallizing proteins by metal-mediated synthetic symmetrization.
Authors: Laganowsky, A. / Zhao, M. / Soriaga, A.B. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
History
DepositionJun 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Jan 28, 2015Group: Other
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_ref_seq_dif.details / _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
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6114
Polymers18,5041
Non-polymers1063
Water4,450247
1
C: Lysozyme
hetero molecules

C: Lysozyme
hetero molecules

C: Lysozyme
hetero molecules

C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,44216
Polymers74,0174
Non-polymers42512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_555x,-y,-z1
Buried area6210 Å2
ΔGint-151 kcal/mol
Surface area28860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.988, 83.988, 58.923
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number89
Space group name H-MP422
Components on special symmetry positions
IDModelComponents
11C-170-

HOH

21C-179-

HOH

-
Components

#1: Protein Lysozyme / Endolysin / Lysis protein / Muramidase


Mass: 18504.221 Da / Num. of mol.: 1 / Mutation: C54T, R76C, R80C, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4.3M Sodium Chloride, 0.1M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.43→80 Å / Num. obs: 38885 / % possible obs: 99.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.063 / Χ2: 0.876 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.43-1.485.40.53438391.181100
1.48-1.545.40.36638491.1221100
1.54-1.615.40.26838481.0721100
1.61-1.75.40.18838650.9621100
1.7-1.85.40.1438630.8961100
1.8-1.945.40.11638870.9771100
1.94-2.145.40.09739020.8771100
2.14-2.455.40.08339290.8591100
2.45-3.085.30.0539710.465199.8
3.08-805.20.03539320.338193.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.434→48.236 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.908 / SU ML: 0.14 / σ(F): 0 / Phase error: 15.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1775 1958 5.04 %
Rwork0.1391 --
obs0.141 38858 99.07 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.45 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso max: 54.98 Å2 / Biso mean: 20.2316 Å2 / Biso min: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.0474 Å20 Å2-0 Å2
2--1.0474 Å2-0 Å2
3----2.0947 Å2
Refinement stepCycle: LAST / Resolution: 1.434→48.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 0 3 247 1527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011346
X-RAY DIFFRACTIONf_angle_d1.2221828
X-RAY DIFFRACTIONf_chiral_restr0.073208
X-RAY DIFFRACTIONf_plane_restr0.005235
X-RAY DIFFRACTIONf_dihedral_angle_d12.386514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.434-1.46990.22181390.17112535267497
1.4699-1.50970.20871230.148626172740100
1.5097-1.55410.18491310.127526372768100
1.5541-1.60430.19271470.116225912738100
1.6043-1.66160.15811360.108226092745100
1.6616-1.72810.15451320.109726352767100
1.7281-1.80680.1721510.10326252776100
1.8068-1.9020.17481420.114626402782100
1.902-2.02120.17181380.118426392777100
2.0212-2.17730.17111460.118526632809100
2.1773-2.39640.18471480.137126462794100
2.3964-2.74310.20591450.153426872832100
2.7431-3.45590.17231480.154927172865100
3.4559-48.26340.16541320.15482659279192

+
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