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- PDB-4ols: The amidase-2 domain of LysGH15 -

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Basic information

Entry
Database: PDB / ID: 4ols
TitleThe amidase-2 domain of LysGH15
ComponentsEndolysin
KeywordsHYDROLASE / amidase-2 domain
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 / Lysozyme-like / Peptidoglycan recognition protein-like / 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 / Lysozyme-like / Peptidoglycan recognition protein-like / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Endolysin LysGH15
Similarity search - Component
Biological speciesStaphylococcus phage GH15 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 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 1.0Jun 4, 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_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_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: Endolysin
B: Endolysin
C: Endolysin
D: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,56823
Polymers106,3764
Non-polymers1,19219
Water11,530640
1
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8565
Polymers26,5941
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9216
Polymers26,5941
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9216
Polymers26,5941
Non-polymers3275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8706
Polymers26,5941
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.400, 135.400, 107.077
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Endolysin / Putative lysin


Mass: 26594.031 Da / Num. of mol.: 4 / Fragment: amidase-2 domain, UNP RESIDUES 165-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage GH15 (virus) / Gene: lysGH15, GH15_071 / Production host: Escherichia coli (E. coli) / References: UniProt: D6QY02
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris-HCl, pH 9.0, 0.2M Li2SO4, 30% (wt/vol) PEG 3000, 0.1M xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Oct 16, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. all: 48572 / Num. obs: 48572 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.27→50 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.27→39.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.786 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1608 2595 5.1 %RANDOM
Rwork0.15756 ---
all0.15773 48572 --
obs0.15773 48572 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.48 Å2-0 Å2
2--0.48 Å2-0 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.27→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5868 0 19 640 6527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196056
X-RAY DIFFRACTIONr_bond_other_d00.025632
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9168164
X-RAY DIFFRACTIONr_angle_other_deg3.535312948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.545752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52724.211304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.502151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2481532
X-RAY DIFFRACTIONr_chiral_restr0.0860.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027052
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021548
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7532.5812972
X-RAY DIFFRACTIONr_mcbond_other2.7532.5792971
X-RAY DIFFRACTIONr_mcangle_it3.9563.8433712
X-RAY DIFFRACTIONr_mcangle_other3.9553.8453713
X-RAY DIFFRACTIONr_scbond_it4.22.9173084
X-RAY DIFFRACTIONr_scbond_other4.1992.9193085
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1594.1754445
X-RAY DIFFRACTIONr_long_range_B_refined7.92522.1217432
X-RAY DIFFRACTIONr_long_range_B_other7.63421.247168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.274→2.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 209 -
Rwork0.172 3538 -
obs--98.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37480.16950.22990.31750.09860.4994-0.0324-0.07010.06320.0064-0.00230.02720.03210.00390.03470.108-0.0052-0.02120.049-0.04140.065283.814813.247829.1477
20.3063-0.18460.21080.44710.20.74520.11810.07810.0573-0.0678-0.0614-0.04280.23370.1295-0.05660.16490.12760.00470.11170.02170.054648.724722.91962.7288
30.20440.0656-0.13360.6309-0.13860.72650.00210.00140.00930.07760.0508-0.052-0.1461-0.0927-0.05290.13830.041-0.00960.04480.03940.068751.422714.393156.036
40.2478-0.06460.03090.30010.2110.88110.01920.0093-0.01720.00940.0306-0.05260.0948-0.1048-0.04970.1034-0.0297-0.01210.04720.02740.078553.6928-4.46329.5914
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A189 - 373
2X-RAY DIFFRACTION2B189 - 373
3X-RAY DIFFRACTION3C189 - 373
4X-RAY DIFFRACTION4D189 - 373

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