[English] 日本語
Yorodumi
- PDB-4olk: The CHAP domain of LysGH15 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4olk
TitleThe CHAP domain of LysGH15
ComponentsEndolysin
KeywordsHYDROLASE / CHAP
Function / homology
Function and homology information


N-acetylmuramoyl-L-alanine amidase activity / viral release from host cell by cytolysis / peptidoglycan catabolic process / defense response to bacterium / metal ion binding
Similarity search - Function
Bacterial SH3 domain / Bacterial SH3 domain homologues / CHAP domain profile. / CHAP domain / CHAP domain / SH3-like domain, bacterial-type / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Ami_2 / N-acetylmuramoyl-L-alanine amidase ...Bacterial SH3 domain / Bacterial SH3 domain homologues / CHAP domain profile. / CHAP domain / CHAP domain / SH3-like domain, bacterial-type / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus phage GH15 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.694 Å
AuthorsGu, J. / Ouyang, S. / Liu, Z.J. / Han, W.
CitationJournal: Plos Pathog. / Year: 2014
Title: Structural and biochemical characterization reveals LysGH15 as an unprecedented "EF-hand-like" calcium-binding phage lysin.
Authors: Gu, J. / Feng, Y. / Feng, X. / Sun, C. / Lei, L. / Ding, W. / Niu, F. / Jiao, L. / Yang, M. / Li, Y. / Liu, X. / Song, J. / Cui, Z. / Han, D. / Du, C. / Yang, Y. / Ouyang, S. / Liu, Z.J. / Han, W.
History
DepositionJan 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
A: Endolysin
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1555
Polymers37,7922
Non-polymers3623
Water2,810156
1
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2193
Polymers18,8961
Non-polymers3222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9362
Polymers18,8961
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.359, 113.359, 178.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein Endolysin / Putative lysin


Mass: 18896.119 Da / Num. of mol.: 2 / Fragment: CHAP, UNP RESIDUES 1-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage GH15 (virus) / Gene: GH15_071, lysGH15, phage / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D6QY02
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 4.38 Å3/Da / Density % sol: 71.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Bis-Tris-propane, pH 7.5, 3.8M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 18004 / Num. obs: 18004 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
DMmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.694→47.849 Å / SU ML: 0.11 / σ(F): 1.35 / Phase error: 19.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 1801 10 %RANDOM
Rwork0.1737 ---
all0.1775 18004 --
obs0.1775 18004 92.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.694→47.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 21 156 2804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112727
X-RAY DIFFRACTIONf_angle_d0.8383704
X-RAY DIFFRACTIONf_dihedral_angle_d15.074993
X-RAY DIFFRACTIONf_chiral_restr0.064381
X-RAY DIFFRACTIONf_plane_restr0.004465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6935-2.76630.31061380.236124495
2.7663-2.84770.26031360.2395122895
2.8477-2.93960.30111390.2132124595
2.9396-3.04470.23061370.2186123494
3.0447-3.16660.24941390.1912125094
3.1666-3.31060.23471370.1914122894
3.3106-3.48510.2021360.1724123293
3.4851-3.70340.18021390.1466124893
3.7034-3.98920.17841380.1421123793
3.9892-4.39040.13571370.1294123992
4.3904-5.02510.14931380.1268124391
5.0251-6.32880.21341400.1908125990
6.3288-47.85690.23751470.2109131688
Refinement TLS params.Method: refined / Origin x: -38.6532 Å / Origin y: -5.9031 Å / Origin z: 17.0174 Å
111213212223313233
T0.1319 Å20.1032 Å2-0.0204 Å2--0.0309 Å20.0614 Å2--0.0301 Å2
L0.2095 °2-0.0997 °20.1054 °2-0.4054 °2-0.0798 °2--0.3553 °2
S-0.0846 Å °0.0133 Å °0.0238 Å °0.0504 Å °-0.0079 Å °0.0117 Å °0.0353 Å °0.1472 Å °0.0283 Å °
Refinement TLS groupSelection details: ALL

+
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://pdbjlvh1.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