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- PDB-7dws: The structure of T4 Lysozyme I3C/C54T/R125C/E128C complex with Zi... -

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Basic information

Entry
Database: PDB / ID: 7dws
TitleThe structure of T4 Lysozyme I3C/C54T/R125C/E128C complex with Zinc ions
ComponentsEndolysin
KeywordsHYDROLASE / muramidase / enzyme / mutant / metal ion / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


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
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, X. / Chen, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81902199 China
CitationJournal: Biomaterials / Year: 2021
Title: Rationally designed protein cross-linked hydrogel for bone regeneration via synergistic release of magnesium and zinc ions.
Authors: Chen, X. / Tan, B. / Wang, S. / Tang, R. / Bao, Z. / Chen, G. / Chen, S. / Tang, W. / Wang, Z. / Long, C. / Lu, W.W. / Yang, D. / Bian, L. / Peng, S.
History
DepositionJan 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin
B: Endolysin
C: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7517
Polymers58,4893
Non-polymers2624
Water1629
1
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5622
Polymers19,4961
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8510 Å2
MethodPISA
2
B: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6273
Polymers19,4961
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-19 kcal/mol
Surface area7720 Å2
MethodPISA
3
C: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5622
Polymers19,4961
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-17 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.861, 102.861, 244.533
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-305-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resseq 0 or (resid 1 and (name...
21(chain B and (resseq 0:12 or (resid 13 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain C and (resseq 0 or (resid 1 and (name...CC05
12METMETMETMET(chain C and (resseq 0 or (resid 1 and (name...CC16
13SERSERLYSLYS(chain C and (resseq 0 or (resid 1 and (name...CC0 - 1625 - 167
14SERSERLYSLYS(chain C and (resseq 0 or (resid 1 and (name...CC0 - 1625 - 167
21SERSERGLYGLY(chain B and (resseq 0:12 or (resid 13 and (name...BB0 - 125 - 17
22LEULEULEULEU(chain B and (resseq 0:12 or (resid 13 and (name...BB1318
23GLYGLYTYRTYR(chain B and (resseq 0:12 or (resid 13 and (name...BB-1 - 1614 - 166
24GLYGLYTYRTYR(chain B and (resseq 0:12 or (resid 13 and (name...BB-1 - 1614 - 166
25GLYGLYTYRTYR(chain B and (resseq 0:12 or (resid 13 and (name...BB-1 - 1614 - 166
26GLYGLYTYRTYR(chain B and (resseq 0:12 or (resid 13 and (name...BB-1 - 1614 - 166

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Components

#1: Protein Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 19496.316 Da / Num. of mol.: 3 / Mutation: I3C,C54T,R125C,E128C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D9IEF7, lysozyme
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.01 mM CoCl2, 0.1 M MES, pH 6.2, 2.2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→19.865 Å / Num. obs: 16874 / % possible obs: 92 % / Redundancy: 1.9 % / Biso Wilson estimate: 74.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.042 / Rrim(I) all: 0.059 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.951.90.153504426150.9380.1530.2173.796.4
8.85-19.861.80.0328254530.9950.0320.04623.172.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SB5

3sb5


Resolution: 2.8→19.86 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 3.41 / Phase error: 41.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.345 1590 9.45 %
Rwork0.3301 15228 -
obs0.3316 16818 85.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.48 Å2 / Biso mean: 99.6258 Å2 / Biso min: 68.91 Å2
Refinement stepCycle: final / Resolution: 2.8→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 4 12 2986
Biso mean--83.92 85.05 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053012
X-RAY DIFFRACTIONf_angle_d0.8234096
X-RAY DIFFRACTIONf_chiral_restr0.051489
X-RAY DIFFRACTIONf_plane_restr0.006528
X-RAY DIFFRACTIONf_dihedral_angle_d14.1521774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C810X-RAY DIFFRACTION10.588TORSIONAL
12B810X-RAY DIFFRACTION10.588TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.89020.44511550.3782145293
2.8902-2.99310.4011410.3571146893
2.9931-3.11260.4061490.3944147393
3.1126-3.25360.39871580.3488141090
3.2536-3.42430.41911480.387143090
3.4243-3.63770.44391410.4063142789
3.6377-3.91660.42071530.3602136987
3.9166-4.30710.36951390.3152136184
4.3071-4.9220.3191580.2918129281
4.922-6.17020.34451210.3445129577
6.1702-19.860.2441270.244125170
Refinement TLS params.Method: refined / Origin x: -35.2088 Å / Origin y: 22.9309 Å / Origin z: -29.5737 Å
111213212223313233
T1.6612 Å2-0.9314 Å20.0401 Å2-0.4577 Å20.0509 Å2--0.6704 Å2
L0.1492 °2-0.4342 °20.0458 °2-0.5559 °2-0.2702 °2--0.2859 °2
S-0.1133 Å °-0.0311 Å °0.1595 Å °0.1995 Å °0.1584 Å °-0.1455 Å °-0.1257 Å °0.2949 Å °0.412 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 162
2X-RAY DIFFRACTION1allB-1 - 161
3X-RAY DIFFRACTION1allC0 - 162
4X-RAY DIFFRACTION1allD1 - 5
5X-RAY DIFFRACTION1allE5 - 23

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