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- PDB-4csh: Native structure of the lytic CHAPK domain of the endolysin LysK ... -

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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 / N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / defense response to bacterium / proteolysis / metal ion binding
Similarity search - Function
Bacterial SH3 domain / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / CHAP domain profile. / CHAP domain / CHAP domain / 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 / SH3-like domain, bacterial-type / CHAP domain profile. / CHAP domain / CHAP domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Details

Sequence detailsCHAPK DOMAIN COMPRISING FIRST 165 AMINO ACIDS.

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Experimental details

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Experiment

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

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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

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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

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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 %

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