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- PDB-7sj6: T4 Lysozyme L99A/M102H with 1,2-Azaborine bound -

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Basic information

Entry
Database: PDB / ID: 7sj6
TitleT4 Lysozyme L99A/M102H with 1,2-Azaborine bound
ComponentsLysozyme
KeywordsHYDROLASE / Organism(s): Escherichia virus T4
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
Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / 1,2-dihydro-1,2-azaborinine / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsYao, L. / Wirth, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01-GM094541 United States
CitationJournal: to be published
Title: T4 Lysozyme L99A/M102H with 1,2-Azaborine bound
Authors: Yao, L. / Wirth, J.
History
DepositionOct 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 29, 2023Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,81713
Polymers42,8092
Non-polymers1,00811
Water8,989499
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9086
Polymers21,4041
Non-polymers5035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9097
Polymers21,4041
Non-polymers5046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.780, 75.840, 52.820
Angle α, β, γ (deg.)90.000, 93.223, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 21404.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00720, lysozyme

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Non-polymers , 6 types, 510 molecules

#2: Chemical ChemComp-B20 / 1,2-dihydro-1,2-azaborinine / 1,2-DIHYDRO-1,2-AZABORINE / 1,2-Dihydro-1,2-azaborine


Mass: 78.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6BN / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown from a 5 mg/ml solution of the protein by the hanging drop method at 4 oC over a well solution of 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3 % ...Details: Crystals were grown from a 5 mg/ml solution of the protein by the hanging drop method at 4 oC over a well solution of 0.1 M sodium acetate, pH 4.5, 30% (w/v) PEG-6000, 0.3 M LiSO4, 3 % trimethylamine N-oxide, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.72→52.74 Å / Num. obs: 34602 / % possible obs: 84.9 % / Redundancy: 3.05 % / Biso Wilson estimate: 19.35 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.064 / Net I/σ(I): 14.5
Reflection shellResolution: 1.721→1.783 Å / Redundancy: 1.86 % / Mean I/σ(I) obs: 1.34 / Num. unique obs: 1518 / CC1/2: 0.666 / Rrim(I) all: 0.644 / % possible all: 37.76

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 181L

181l


Resolution: 1.72→52.74 Å / SU ML: 0.1517 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1993
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2015 1770 5.12 %
Rwork0.1686 32831 -
obs0.1703 34601 84.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.49 Å2
Refinement stepCycle: LAST / Resolution: 1.72→52.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 57 499 3329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352874
X-RAY DIFFRACTIONf_angle_d0.59333868
X-RAY DIFFRACTIONf_chiral_restr0.0355421
X-RAY DIFFRACTIONf_plane_restr0.0025496
X-RAY DIFFRACTIONf_dihedral_angle_d14.21781065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.770.2858560.24311053X-RAY DIFFRACTION35.64
1.77-1.820.2491760.23461438X-RAY DIFFRACTION48.51
1.82-1.880.3018730.22021821X-RAY DIFFRACTION60.59
1.88-1.950.28841180.20542198X-RAY DIFFRACTION74.45
1.95-2.020.23231310.20222605X-RAY DIFFRACTION87.95
2.02-2.120.20371670.17232943X-RAY DIFFRACTION98.36
2.12-2.230.17391580.16062911X-RAY DIFFRACTION99.26
2.23-2.370.20291660.15992971X-RAY DIFFRACTION99.68
2.37-2.550.21531530.16372956X-RAY DIFFRACTION99.58
2.55-2.810.19181620.17142984X-RAY DIFFRACTION99.81
2.81-3.210.1991980.17472932X-RAY DIFFRACTION99.9
3.21-4.050.19751540.1492987X-RAY DIFFRACTION99.34
4.05-52.740.18181580.16283032X-RAY DIFFRACTION99.63

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