[English] 日本語
Yorodumi
- PDB-5d74: The crystal structure of Ly7917 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5d74
TitleThe crystal structure of Ly7917
ComponentsPutative phage lysin
KeywordsHYDROLASE / endolysin / prophage / Lytic activity
Function / homologyBacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / CHAP domain profile. / CHAP domain / CHAP domain / SH3-like domain, bacterial-type / Papain-like cysteine peptidase superfamily / Putative phage lysin
Function and homology information
Biological speciesStreptococcus phage phi7917 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWu, L. / Ji, W.H. / Sun, J.H. / Zhou, J.H.
CitationJournal: To Be Published
Title: The crystal structure of Ly7917
Authors: Wu, L. / Ji, W.H. / Sun, J.H. / Zhou, J.H.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative phage lysin
B: Putative phage lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,08215
Polymers58,7082
Non-polymers37413
Water8,881493
1
A: Putative phage lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6009
Polymers29,3541
Non-polymers2468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area10810 Å2
MethodPISA
2
B: Putative phage lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4826
Polymers29,3541
Non-polymers1275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.009, 97.701, 174.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

-
Components

#1: Protein Putative phage lysin / lysin


Mass: 29354.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage phi7917 (virus) / Gene: phi7917_002 / Plasmid: pSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: M1PKZ3
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris, 0.8M LiCl / PH range: 6.5-7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 47363 / % possible obs: 99.8 % / Redundancy: 13.1 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 11.9 %

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→34.643 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 2368 5.05 %
Rwork0.1958 --
obs0.1977 46869 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→34.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 13 493 4028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073636
X-RAY DIFFRACTIONf_angle_d1.0114964
X-RAY DIFFRACTIONf_dihedral_angle_d12.3691264
X-RAY DIFFRACTIONf_chiral_restr0.042541
X-RAY DIFFRACTIONf_plane_restr0.004646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8988-1.93760.32921180.26262254X-RAY DIFFRACTION85
1.9376-1.97970.33891280.26222434X-RAY DIFFRACTION94
1.9797-2.02570.28921400.24282543X-RAY DIFFRACTION97
2.0257-2.07640.30251360.23762615X-RAY DIFFRACTION98
2.0764-2.13250.29241480.22792614X-RAY DIFFRACTION100
2.1325-2.19530.27941470.22552616X-RAY DIFFRACTION100
2.1953-2.26610.26531520.21982618X-RAY DIFFRACTION100
2.2661-2.34710.27051390.21612632X-RAY DIFFRACTION100
2.3471-2.4410.24471280.20312677X-RAY DIFFRACTION100
2.441-2.55210.26331310.21032621X-RAY DIFFRACTION99
2.5521-2.68660.25451420.21392669X-RAY DIFFRACTION100
2.6866-2.85480.23411500.22192645X-RAY DIFFRACTION100
2.8548-3.07510.2831370.20952673X-RAY DIFFRACTION100
3.0751-3.38440.22811390.19432653X-RAY DIFFRACTION100
3.3844-3.87350.19391710.16722682X-RAY DIFFRACTION100
3.8735-4.87810.15071190.14322728X-RAY DIFFRACTION100
4.8781-34.6490.17591430.16242827X-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