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- PDB-5d76: The crystal structure of Ly7917 with the hydrolyzing product of MDP -

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Basic information

Entry
Database: PDB / ID: 5d76
TitleThe crystal structure of Ly7917 with the hydrolyzing product of MDP
ComponentsPutative phage lysin
KeywordsHYDROLASE / endolysin / prophage / Lytic activity
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / N-acetylmuramoyl-L-alanine amidase / catalytic activity
Similarity search - Function
Bacterial SH3 domain / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / CHAP domain profile. / CHAP domain / CHAP domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
L-alanyl-D-alpha-glutamine / N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesStreptococcus phage phi7917 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsWu, L. / Ji, W.H. / Sun, J.H. / Zhou, J.H.
CitationJournal: To Be Published
Title: The crystal structure of Ly7917
Authors: Wu, L. / Ji, W.H. / Sun, J.H. / Zhou, J.H.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phage lysin
B: Putative phage lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2146
Polymers58,7082
Non-polymers5054
Water45025
1
A: Putative phage lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6424
Polymers29,3541
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area10650 Å2
MethodPISA
2
B: Putative phage lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5712
Polymers29,3541
Non-polymers2171
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.856, 97.139, 174.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative phage lysin / lysin


Mass: 29354.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage phi7917 (virus) / Gene: phi7917_002 / Plasmid: pSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: M1PKZ3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-58B / L-alanyl-D-alpha-glutamine


Mass: 217.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15N3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M Na-tartrate, 1.2M NaCl / PH range: 5.0-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Apr 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 20090 / % possible obs: 100 % / Redundancy: 11.9 % / Net I/σ(I): 20.4
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 61.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D74

5d74


Resolution: 2.54→37.283 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2657 963 4.81 %
Rwork0.2074 --
obs0.2103 20019 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→37.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 32 25 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113657
X-RAY DIFFRACTIONf_angle_d1.2044996
X-RAY DIFFRACTIONf_dihedral_angle_d14.8311250
X-RAY DIFFRACTIONf_chiral_restr0.056543
X-RAY DIFFRACTIONf_plane_restr0.005650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5353-2.66890.35621270.28462642X-RAY DIFFRACTION98
2.6689-2.83610.31511340.29012713X-RAY DIFFRACTION100
2.8361-3.0550.36881040.28592706X-RAY DIFFRACTION100
3.055-3.36230.36891630.23372705X-RAY DIFFRACTION100
3.3623-3.84830.26611380.20142724X-RAY DIFFRACTION100
3.8483-4.84680.21421570.16132733X-RAY DIFFRACTION100
4.8468-37.28710.22441400.19032833X-RAY DIFFRACTION99

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