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- PDB-4jz5: High-resolution structure of catalytic domain of endolysin ply40 ... -

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Basic information

Entry
Database: PDB / ID: 4jz5
TitleHigh-resolution structure of catalytic domain of endolysin ply40 from bacteriophage P40 of Listeria monocytogenes
ComponentsGp26
KeywordsHYDROLASE / Endolysin / Glycosyl hydrolase family 25 / Peptidoglycan / cell-wall
Function / homology
Function and homology information


peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme activity
Similarity search - Function
Bacterial SH3 domain / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. ...Bacterial SH3 domain / Glycoside hydrolase, family 25 / Glycosyl hydrolases family 25 / SH3b domain profile. / Bacterial SH3 domain homologues / SH3-like domain, bacterial-type / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria phage P40 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsRomero-Fernandez, P. / Bartual, S.G. / Carrasco-lopez, C. / Hermoso, J.A.
CitationJournal: To be Published
Title: Crystal structure of catalytic domain of endolysin Ply40
Authors: Romero-Fernandez, P. / Bartual, S.G. / Carrasco-lopez, C. / Loessner, M. / Hermoso, J.A.
History
DepositionApr 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gp26


Theoretical massNumber of molelcules
Total (without water)25,0791
Polymers25,0791
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.332, 42.332, 98.627
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Gp26 / ply40


Mass: 25078.514 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 1-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage P40 (virus) / Gene: gp26 / Production host: Escherichia coli (E. coli) / References: UniProt: B6D7J9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growpH: 7 / Details: 0.2M Sodium Malonate, 20%(w/v) PEG, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2011
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.1→36.661 Å / Num. all: 78926 / Num. obs: 78926 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.1→1.12 Å / % possible all: 80

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1063)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HMC

3hmc


Resolution: 1.1→36.661 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.07 / σ(F): 1.98 / Phase error: 12.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1428 3950 5.01 %RANDOM
Rwork0.1344 ---
all0.1348 78870 --
obs0.1348 78870 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.39 Å2 / Biso mean: 11.511 Å2 / Biso min: 3.53 Å2
Refinement stepCycle: LAST / Resolution: 1.1→36.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 0 345 1975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071713
X-RAY DIFFRACTIONf_angle_d1.2292320
X-RAY DIFFRACTIONf_chiral_restr0.073245
X-RAY DIFFRACTIONf_plane_restr0.006302
X-RAY DIFFRACTIONf_dihedral_angle_d12.187638
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11340.24261020.21922220232278
1.1134-1.12750.21341100.20082317242786
1.1275-1.14240.17811350.18592531266692
1.1424-1.1580.17811250.16842555268095
1.158-1.17450.17281520.16022742289499
1.1745-1.19210.1641430.152426932836100
1.1921-1.21070.1651510.146827262877100
1.2107-1.23060.14981560.144826802836100
1.2306-1.25180.17021450.140827462891100
1.2518-1.27450.15861510.134727232874100
1.2745-1.29910.13341130.132427272840100
1.2991-1.32560.15371460.133627592905100
1.3256-1.35440.13771490.128226752824100
1.3544-1.38590.12671390.126927572896100
1.3859-1.42060.12981540.126326862840100
1.4206-1.4590.16091600.120927612921100
1.459-1.50190.13031480.119626982846100
1.5019-1.55040.1151330.113827252858100
1.5504-1.60580.1391330.11327072840100
1.6058-1.67010.13281420.118427392881100
1.6701-1.74610.11681390.115827212860100
1.7461-1.83820.13081660.123527412907100
1.8382-1.95330.12481270.120327142841100
1.9533-2.10410.12151570.122327252882100
2.1041-2.31580.12441430.12526992842100
2.3158-2.65090.15391380.135727502888100
2.6509-3.33950.15231530.141126972850100
3.3395-36.68090.14251400.14392706284699
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)
12.3274-1.6260.91751.5382-0.65850.3624-0.1148-0.50660.03040.03850.15440.1515-0.0153-0.21840.00740.0673-0.007-0.00310.12130.00110.0594-15.78386.29836.4507
21.6432-0.21511.16252.1328-0.17942.3130.0835-0.0973-0.05160.2439-0.04950.07980.1042-0.0303-0.07550.0901-0.0192-0.00390.046-0.00090.025-5.8326-3.79159.0661
31.86091.0665-0.18271.3309-0.26590.56230.0439-0.0062-0.1350.0564-0.0387-0.12720.04760.0543-0.00760.052-0.0052-0.01030.041-0.00780.0363.7876-0.06911.6434
42.85293.10090.7184.38420.86220.7145-0.06470.1601-0.2427-0.07770.075-0.27970.0580.0842-0.00960.0502-0.00460.00670.0653-0.01880.057910.05461.7998-7.5106
51.06830.40130.00141.12870.00370.61070.0095-0.00650.0260.0093-0.0002-0.0783-0.06370.0792-0.01490.0537-0.01650.00030.0556-0.00180.0357.591911.9121-5.3446
61.43310.2641-0.2143.04180.8731.34430.0616-0.04040.15350.01020.00020.033-0.2190.04090.0460.0566-0.01880.01310.04590.0010.05540.507416.73580.1749
70.74470.09710.17330.68020.04360.41780.04850.02440.17340.03960.0410.0032-0.18990.042-0.05590.0758-0.01430.01450.038-0.00340.0621-1.126218.49080.8009
80.8468-0.62870.55111.7050.08233.08180.0465-0.03380.11510.12020.0760.1438-0.1943-0.1464-0.10660.06660.00420.02450.0495-0.00130.0717-9.077516.18478.2319
92.04270.88991.46924.08260.31193.58480.0521-0.116-0.03080.2986-0.00150.23710.2437-0.029-0.020.10510.0040.00340.08110.01040.038-6.36360.819116.1541
102.96-0.30010.39952.84470.45082.40630.02010.17840.018-0.2014-0.01750.1624-0.0562-0.23610.00850.0367-0.0148-0.0030.060.01280.0548-12.01848.274-1.6963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -3:7 )A-3 - 7
2X-RAY DIFFRACTION2( CHAIN A AND RESID 8:24 )A8 - 24
3X-RAY DIFFRACTION3( CHAIN A AND RESID 25:65 )A25 - 65
4X-RAY DIFFRACTION4( CHAIN A AND RESID 66:86 )A66 - 86
5X-RAY DIFFRACTION5( CHAIN A AND RESID 87:122 )A87 - 122
6X-RAY DIFFRACTION6( CHAIN A AND RESID 123:137 )A123 - 137
7X-RAY DIFFRACTION7( CHAIN A AND RESID 138:156 )A138 - 156
8X-RAY DIFFRACTION8( CHAIN A AND RESID 157:174 )A157 - 174
9X-RAY DIFFRACTION9( CHAIN A AND RESID 175:186 )A175 - 186
10X-RAY DIFFRACTION10( CHAIN A AND RESID 187:202 )A187 - 202

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