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- PDB-4olk: The CHAP domain of LysGH15 -

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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 / N-acetylmuramoyl-L-alanine amidase activity / viral release from host cell by cytolysis / peptidoglycan catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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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: 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

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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

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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

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