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- PDB-5d74: The crystal structure of Ly7917 -

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Basic information

Entry
Database: PDB / ID: 5d74
TitleThe crystal structure of Ly7917
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
N-acetylmuramoyl-L-alanine amidase
Similarity search - Component
Biological speciesStreptococcus phage phi7917 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,08215
Polymers58,7082
Non-polymers37413
Water8,881493
1
A: Putative phage lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6009
Polymers29,3541
Non-polymers2468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area10810 Å2
MethodPISA
2
B: Putative phage lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4826
Polymers29,3541
Non-polymers1275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.009, 97.701, 174.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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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.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Tris, 0.8M LiCl / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 47363 / % possible obs: 99.8 % / Redundancy: 13.1 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 11.9 %

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→34.643 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 2368 5.05 %
Rwork0.1958 --
obs0.1977 46869 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→34.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 13 493 4028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073636
X-RAY DIFFRACTIONf_angle_d1.0114964
X-RAY DIFFRACTIONf_dihedral_angle_d12.3691264
X-RAY DIFFRACTIONf_chiral_restr0.042541
X-RAY DIFFRACTIONf_plane_restr0.004646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8988-1.93760.32921180.26262254X-RAY DIFFRACTION85
1.9376-1.97970.33891280.26222434X-RAY DIFFRACTION94
1.9797-2.02570.28921400.24282543X-RAY DIFFRACTION97
2.0257-2.07640.30251360.23762615X-RAY DIFFRACTION98
2.0764-2.13250.29241480.22792614X-RAY DIFFRACTION100
2.1325-2.19530.27941470.22552616X-RAY DIFFRACTION100
2.1953-2.26610.26531520.21982618X-RAY DIFFRACTION100
2.2661-2.34710.27051390.21612632X-RAY DIFFRACTION100
2.3471-2.4410.24471280.20312677X-RAY DIFFRACTION100
2.441-2.55210.26331310.21032621X-RAY DIFFRACTION99
2.5521-2.68660.25451420.21392669X-RAY DIFFRACTION100
2.6866-2.85480.23411500.22192645X-RAY DIFFRACTION100
2.8548-3.07510.2831370.20952673X-RAY DIFFRACTION100
3.0751-3.38440.22811390.19432653X-RAY DIFFRACTION100
3.3844-3.87350.19391710.16722682X-RAY DIFFRACTION100
3.8735-4.87810.15071190.14322728X-RAY DIFFRACTION100
4.8781-34.6490.17591430.16242827X-RAY DIFFRACTION100

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