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- PDB-5ewx: Fusion protein of T4 lysozyme and B4 domain of protein A from sta... -

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Basic information

Entry
Database: PDB / ID: 5ewx
TitleFusion protein of T4 lysozyme and B4 domain of protein A from staphylococcal aureus with chemical cross-linker EY-CBS
ComponentsEndolysin,Immunoglobulin G-binding protein A,Endolysin
KeywordsPROTEIN BINDING / Fusion / EY-CBS / alpha helix / cross-linker
Function / homology
Function and homology information


IgG binding / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / extracellular region
Similarity search - Function
Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily ...Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-EYC / Endolysin / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJeong, W.H. / Lee, H. / Song, D.H. / Lee, J.O.
CitationJournal: Nat Commun / Year: 2016
Title: Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker.
Authors: Jeong, W.H. / Lee, H. / Song, D.H. / Eom, J.H. / Kim, S.C. / Lee, H.S. / Lee, H. / Lee, J.O.
History
DepositionNov 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 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: Endolysin,Immunoglobulin G-binding protein A,Endolysin
B: Endolysin,Immunoglobulin G-binding protein A,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4684
Polymers50,4252
Non-polymers1,0432
Water1,15364
1
A: Endolysin,Immunoglobulin G-binding protein A,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7342
Polymers25,2121
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin,Immunoglobulin G-binding protein A,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7342
Polymers25,2121
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.522, 149.850, 55.836
Angle α, β, γ (deg.)90.00, 122.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Endolysin,Immunoglobulin G-binding protein A,Endolysin / Lysis protein / Lysozyme / Muramidase / IgG-binding protein A / Staphylococcal protein A


Mass: 25212.469 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-35, 219-266, 38-164
Mutation: A1212V, G1240A, E1258C, K1261A, L1262A, N40C, C54T, C97A, K162A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of T4 lysozyme (residues 1-35), linker GGGGSGGGGS, protein A (B4 domain, residues 212-266), and T4 lysozyme (residues 38-164)
Source: (gene. exp.) Enterobacteria phage T4 (virus), (gene. exp.) Staphylococcus aureus (bacteria)
Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, UniProt: P38507, lysozyme
#2: Chemical ChemComp-EYC / 2,2'-ethyne-1,2-diylbis{5-[(chloroacetyl)amino]benzenesulfonic acid}


Mass: 521.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14Cl2N2O8S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHOR STATES THAT THERE ARE ERRORS AT THESE POSITIONS IN THE SEQUENCE DATABASE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.97 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS. square rod-plate
Crystal growTemperature: 277 K / Method: evaporation / pH: 7.5 / Details: 1.84M Na/K Phosphate, pH 7.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 35397 / % possible obs: 99.1 % / Redundancy: 3.5 % / Net I/σ(I): 18.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LYD, 1DEE

1lyd

1dee


Resolution: 2.6→42.745 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 31.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 3535 9.99 %
Rwork0.2025 --
obs0.2076 35397 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→42.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 60 64 3472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013458
X-RAY DIFFRACTIONf_angle_d1.4934670
X-RAY DIFFRACTIONf_dihedral_angle_d15.91306
X-RAY DIFFRACTIONf_chiral_restr0.056508
X-RAY DIFFRACTIONf_plane_restr0.011608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.63570.36521320.32231167X-RAY DIFFRACTION82
2.6357-2.67330.38091270.30741180X-RAY DIFFRACTION92
2.6733-2.71320.35041390.30581298X-RAY DIFFRACTION93
2.7132-2.75560.31541400.30631242X-RAY DIFFRACTION94
2.7556-2.80080.33361450.28641299X-RAY DIFFRACTION93
2.8008-2.84910.35921330.25681210X-RAY DIFFRACTION94
2.8491-2.90090.33511490.25191314X-RAY DIFFRACTION94
2.9009-2.95670.31731400.26311262X-RAY DIFFRACTION94
2.9567-3.0170.33831370.26571251X-RAY DIFFRACTION94
3.017-3.08260.33221430.27211276X-RAY DIFFRACTION94
3.0826-3.15430.3431430.27941270X-RAY DIFFRACTION95
3.1543-3.23310.28281470.24521279X-RAY DIFFRACTION95
3.2331-3.32050.31311470.24381330X-RAY DIFFRACTION94
3.3205-3.41820.26871410.21221221X-RAY DIFFRACTION95
3.4182-3.52840.24581420.1921295X-RAY DIFFRACTION94
3.5284-3.65450.22341440.18581281X-RAY DIFFRACTION95
3.6545-3.80070.21361460.16931338X-RAY DIFFRACTION96
3.8007-3.97360.24251390.15941256X-RAY DIFFRACTION95
3.9736-4.18290.18871380.15341282X-RAY DIFFRACTION96
4.1829-4.44470.20351480.15621321X-RAY DIFFRACTION96
4.4447-4.78750.2281380.14831279X-RAY DIFFRACTION96
4.7875-5.26850.21811450.16361335X-RAY DIFFRACTION97
5.2685-6.0290.22071470.19111296X-RAY DIFFRACTION97
6.029-7.5890.19091480.19031325X-RAY DIFFRACTION97
7.589-42.75070.22461370.17621255X-RAY DIFFRACTION92
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)
11.2733-1.03950.81823.6944-1.31851.919-0.0625-0.23050.2068-0.06530.14840.1493-0.2039-0.0624-0.07830.5518-0.02150.11650.3477-0.01150.317791.202711.6323156.7791
22.564-1.42140.15492.2658-0.36820.8980.0618-0.0492-0.03710.0510.05540.0240.1479-0.1756-0.10810.4461-0.01540.0730.3367-0.00960.2298115.0724-20.1956140.0066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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