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- PDB-1h09: Multimodular Pneumococcal Cell Wall Endolysin from phage Cp-1 -

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Basic information

Entry
Database: PDB / ID: 1h09
TitleMultimodular Pneumococcal Cell Wall Endolysin from phage Cp-1
ComponentsLYSOZYME
KeywordsHYDROLASE / MUREIN HYDROLASE / LYSOZYME / MULTIMODULAR / GLYCOSIDASE / BACTERIOLYTIC ENZYME / PNEUMOCOCCAL CELL WALL DEGRADATION
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to bacterium
Similarity search - Function
Multimodular pneumococcal cell wall endolysin, domain 3 / Multimodular pneumococcal cell wall endolysin, domain 3 / Glycosyl hydrolases family 25, active site / Glycosyl hydrolases family 25 active site signature. / Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Cholin Binding ...Multimodular pneumococcal cell wall endolysin, domain 3 / Multimodular pneumococcal cell wall endolysin, domain 3 / Glycosyl hydrolases family 25, active site / Glycosyl hydrolases family 25 active site signature. / Glycoside hydrolase, family 25 subgroup / Glycosyl hydrolases family 25 / Glycosyl hydrolase family 25 (GH25) domain profile. / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / Cholin Binding / left handed beta-beta-3-solenoid / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Single Sheet / Ribbon / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACTERIOPHAGE CP-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsHermoso, J.A. / Monterroso, B. / Albert, A. / Garcia, P. / Menendez, M. / Martinez-Ripoll, M. / Garcia, J.L.
CitationJournal: Structure / Year: 2003
Title: Structural Basis for Selective Recognition of Pneumococcal Cell Wall by Modular Endolysin from Phage Cp-1
Authors: Hermoso, J.A. / Monterroso, B. / Albert, A. / Galan, B. / Ahrazem, O. / Garcia, P. / Martinez-Ripoll, M. / Garcia, J.L. / Menendez, M.
History
DepositionJun 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)39,0901
Polymers39,0901
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.950, 95.780, 129.280
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 LYSOZYME / / MUREIN HYDROLASE / ENDOLYSIN / MURAMIDASE / CP-1 LYSIN


Mass: 39090.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE CP-1 (virus) / Plasmid: PCIP100 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH1 / References: UniProt: P15057, lysozyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN IS A MODULAR ENZYME, THE FIRST RESIDUES (2-188) FORM THE CATALYTIC MODULE, WITH ...THIS PROTEIN IS A MODULAR ENZYME, THE FIRST RESIDUES (2-188) FORM THE CATALYTIC MODULE, WITH RESIDUES 189-199 FORMING THE LINKER AND FINALLY, THE CELL WALL ANCHORING MODULE IS FORMED BY RESIDUES 200-339.

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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: 3.01 Å3/Da / Density % sol: 60 % / Description: SAD WITH A NON-ISOMORPHOUS HG DERIVATIVE
Crystal growpH: 6
Details: 1.7M NA FORMATE, 0.1M NA CIT.(PH6),1.8MM N-DECYL-MALTOSIDE, pH 6.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMTris-HCl1droppH8.0
28 mg/mlprotein1drop
31.7 Msodium formate1reservoir
40.1 Msodium citrate1reservoirpH6.0
51.8 mMn-decyl-beta-D-maltoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.004
DetectorDetector: CCD / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 2.1→39 Å / Num. obs: 28359 / % possible obs: 99.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 39 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
RESOLVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.1→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1701629.16 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1429 5.1 %RANDOM
Rwork0.206 ---
obs0.206 28272 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2--2.13 Å20 Å2
3----3.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 0 326 3089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 246 5.4 %
Rwork0.258 4276 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 7 % / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

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