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- PDB-8aaz: High resolution X-ray analysis of ATP lysozyme complex in the pre... -

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Basic information

Entry
Database: PDB / ID: 8aaz
TitleHigh resolution X-ray analysis of ATP lysozyme complex in the presence of 80 mM ATP
ComponentsLysozyme
KeywordsHYDROLASE / Complex / ligand binding / ATP / lysozyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsZalar, M. / Curtis, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/N024796/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Nonspecific Binding of Adenosine Tripolyphosphate and Tripolyphosphate Modulates the Phase Behavior of Lysozyme.
Authors: Zalar, M. / Bye, J. / Curtis, R.
History
DepositionJul 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Nov 20, 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: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8534
Polymers14,3311
Non-polymers1,5223
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-4 kcal/mol
Surface area6960 Å2
Unit cell
Length a, b, c (Å)78.389, 78.389, 38.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-417-

HOH

31A-445-

HOH

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Components

#1: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10 mM Tris-HCl pH 7.0, 80 mM Na2-ATP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.27→39.19 Å / Num. obs: 31931 / % possible obs: 99.99 % / Redundancy: 51.6 % / Biso Wilson estimate: 12.22 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0516 / Rpim(I) all: 0.007296 / Rrim(I) all: 0.05213 / Net I/σ(I): 50.22
Reflection shellResolution: 1.27→1.315 Å / Redundancy: 50.9 % / Rmerge(I) obs: 0.2322 / Mean I/σ(I) obs: 10.3 / Num. unique obs: 3125 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.03279 / Rrim(I) all: 0.2346 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia23.8.0-g3d570883-tags-v3.8.0-0data reduction
PHASER2.8.3phasing
xia23.8.0-g3d570883-tags-v3.8.0-0data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LZT

2lzt


Resolution: 1.27→39.19 Å / SU ML: 0.1038 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 14.4983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1713 2000 6.26 %
Rwork0.1395 29930 -
obs0.1415 31930 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.96 Å2
Refinement stepCycle: LAST / Resolution: 1.27→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 93 154 1248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671177
X-RAY DIFFRACTIONf_angle_d1.08811624
X-RAY DIFFRACTIONf_chiral_restr0.0999165
X-RAY DIFFRACTIONf_plane_restr0.0106198
X-RAY DIFFRACTIONf_dihedral_angle_d8.6749169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.30.16811400.12022101X-RAY DIFFRACTION99.87
1.3-1.340.1581400.13132081X-RAY DIFFRACTION100
1.34-1.380.21751400.14592112X-RAY DIFFRACTION100
1.38-1.420.17491400.1322100X-RAY DIFFRACTION100
1.42-1.470.17391420.12452119X-RAY DIFFRACTION100
1.47-1.530.16031420.11632113X-RAY DIFFRACTION100
1.53-1.60.15541400.11992102X-RAY DIFFRACTION100
1.6-1.680.14481420.11742125X-RAY DIFFRACTION100
1.68-1.790.19161420.12742120X-RAY DIFFRACTION100
1.79-1.930.14421420.12712136X-RAY DIFFRACTION100
1.93-2.120.16251440.12922148X-RAY DIFFRACTION100
2.12-2.430.14931440.12932159X-RAY DIFFRACTION100
2.43-3.060.17031470.15192192X-RAY DIFFRACTION100
3.06-39.190.19441550.16062322X-RAY DIFFRACTION99.96

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