[English] 日本語
Yorodumi
- PDB-4csh: Native structure of the lytic CHAPK domain of the endolysin LysK ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4csh
TitleNative structure of the lytic CHAPK domain of the endolysin LysK from Staphylococcus aureus bacteriophage K
ComponentsLYSK
KeywordsHYDROLASE / ENDOLYSIN / PEPTIDOGLYCAN / PROTEASE
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / peptidase activity / 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 K (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsSanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J.
Citation
Journal: Virol. J. / Year: 2014
Title: Crystal structure of the lytic CHAP(K) domain of the endolysin LysK from Staphylococcus aureus bacteriophage K.
Authors: Sanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Crystallization of the Chap Domain of the Endolysin from Staphylococcus Aureus Bacteriophage K.
Authors: Sanz-Gaitero, M. / Keary, R. / Garcia-Doval, C. / Coffey, A. / van Raaij, M.J.
#2: Journal: Bacteriophage / Year: 2011
Title: In Silico Modeling of the Staphylococcal Bacteriophage-Derived Peptidase Chap(K).
Authors: Fenton, M. / Cooney, J.C. / Ross, R.P. / Sleator, R.D. / McAuliffe, O. / O'Mahony, J. / Coffey, A.
#3: Journal: Appl.Environ.Microbiol. / Year: 2009
Title: Phage Lysin Lysk Can be Truncated to its Chap Domain and Retain Lytic Activity Against Live Antibiotic-Resistant Staphylococci.
Authors: Horgan, M. / O'Flynn, G. / Garry, J. / Cooney, J. / Coffey, A. / Fitzgerald, G.F. / Ross, R.P. / McAuliffe, O.
History
DepositionMar 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Data collection
Revision 1.2Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: LYSK
B: LYSK
C: LYSK
D: LYSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,83021
Polymers74,4434
Non-polymers1,38717
Water13,349741
1
A: LYSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0276
Polymers18,6111
Non-polymers4165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9355
Polymers18,6111
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LYSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9355
Polymers18,6111
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LYSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9355
Polymers18,6111
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.220, 61.470, 73.130
Angle α, β, γ (deg.)91.49, 98.62, 89.99
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 165 / Label seq-ID: 2 - 165

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.99997, 0.00025, -0.00727), (0.00027, 0.99999, -0.00334), (0.00727, -0.00334, -0.99997)29.354, 30.94843, 126.09038
2given(0.99951, -0.0311, -0.0035), (-0.02633, -0.89611, 0.44306), (-0.01691, -0.44275, -0.89649)-16.69319, -12.97608, 129.98643
3given(-0.99932, 0.03573, 0.00936), (-0.02776, -0.89371, 0.44778), (0.02436, 0.44722, 0.89409)5.92489, 17.41995, -3.9347
4given(-0.99946, -0.03087, 0.01131), (0.02274, -0.89756, -0.44031), (0.02375, -0.43981, 0.89778)12.19289, 69.64667, 29.70509
5given(0.99923, 0.03535, -0.01709), (0.02406, -0.89526, -0.4449), (-0.03103, 0.44414, -0.89542)-22.36007, 100.51833, 96.1291
6given(-0.99997, -0.00165, -0.00794), (-0.00161, 0.99998, -0.0054), (0.00795, -0.00539, -0.99995)-9.78214, 31.06825, 126.10248

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
LYSK


Mass: 18610.824 Da / Num. of mol.: 4 / Fragment: CHAPK, RESIDUES 1-165
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS PHAGE K (virus) / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: Q6Y7T6

-
Non-polymers , 6 types, 758 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsCHAPK DOMAIN COMPRISING FIRST 165 AMINO ACIDS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 6.5
Details: 25 MM TRIS-HCL, 22% (W/V) POLYETHYLENE GLYCOL 8000, 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC ACID-NAOH PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2014
Details: ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.79→36.53 Å / Num. obs: 62028 / % possible obs: 97.2 % / Redundancy: 2 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.3
Reflection shellResolution: 1.79→1.88 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.9 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INTERMEDIATE MODEL BASED ON DERIVATIVE DATA, PDB ENTRY 4CT3

4ct3


Resolution: 1.79→32.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.717 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20106 2338 3.8 %RANDOM, COPIED FROM DERIVATIVE DATA
Rwork0.17486 ---
obs0.17598 59686 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20.64 Å20.53 Å2
2---0.52 Å2-0.16 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.79→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5232 0 66 741 6039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025496
X-RAY DIFFRACTIONr_bond_other_d0.0070.025065
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9347480
X-RAY DIFFRACTIONr_angle_other_deg1.279311702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9745676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78424.606254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09815890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9341516
X-RAY DIFFRACTIONr_chiral_restr0.0860.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026256
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021312
X-RAY DIFFRACTIONr_nbd_refined0.2750.21672
X-RAY DIFFRACTIONr_nbd_other0.1760.24611
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22695
X-RAY DIFFRACTIONr_nbtor_other0.0780.22439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.225
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.2131
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.2104
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2940.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4991.6192644
X-RAY DIFFRACTIONr_mcbond_other1.4981.6182643
X-RAY DIFFRACTIONr_mcangle_it2.4112.423304
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9241.8382852
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0162.6684164
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99020.07
12B99020.07
21A98810.06
22C98810.06
31A98000.07
32D98000.07
41B98210.09
42C98210.09
51B97680.09
52D97680.09
61C98620.05
62D98620.05
LS refinement shellResolution: 1.788→1.884 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.282 112 -
Rwork0.233 8628 -
obs--94.27 %

+
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