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- PDB-7a70: HEW lysozyme in complex with Ti(OH)4 -

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Basic information

Entry
Database: PDB / ID: 7a70
TitleHEW lysozyme in complex with Ti(OH)4
ComponentsLysozyme
KeywordsHYDROLASE / Lysozyme / titanium / biomineralization
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
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-like domain superfamily
Similarity search - Domain/homology
tetrakis(oxidanyl)titanium / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCalderone, V. / Gigli, L. / Ravera, E. / Luchinat, C.
CitationJournal: Biomolecules / Year: 2020
Title: On the Mechanism of Bioinspired Formation of Inorganic Oxides: Structural Evidence of the Electrostatic Nature of the Interaction between a Mononuclear Inorganic Precursor and Lysozyme.
Authors: Gigli, L. / Ravera, E. / Calderone, V. / Luchinat, C.
History
DepositionAug 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6748
Polymers14,3311
Non-polymers3437
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-48 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.090, 78.090, 37.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-375-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 94 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-R3H / tetrakis(oxidanyl)titanium / Titanic acid


Mass: 115.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O4Ti / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 1.98 Å3/Da / Density % sol: 37.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.5 M Tris-HCl, 0.7 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20052 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 2909 / CC1/2: 0.55 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(dev_3965: ???)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w1x

2w1x


Resolution: 1.8→27.61 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 548 5 %
Rwork0.1936 --
obs0.1958 10951 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 14 87 1102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071028
X-RAY DIFFRACTIONf_angle_d0.8921389
X-RAY DIFFRACTIONf_dihedral_angle_d5.837144
X-RAY DIFFRACTIONf_chiral_restr0.056145
X-RAY DIFFRACTIONf_plane_restr0.008181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.980.30361240.27092364X-RAY DIFFRACTION91
1.98-2.270.26251370.21832597X-RAY DIFFRACTION100
2.27-2.850.26151400.20912655X-RAY DIFFRACTION100
2.85-27.610.21081470.16782787X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.8219 Å / Origin y: 20.1644 Å / Origin z: -9.7718 Å
111213212223313233
T0.208 Å2-0.0139 Å2-0.0642 Å2-0.1387 Å20.0267 Å2--0.1891 Å2
L1.1377 °20.3687 °2-0.7818 °2-1.0204 °20.0143 °2--0.7224 °2
S-0.0102 Å °0.0314 Å °-0.0112 Å °0.1335 Å °0.0125 Å °-0.2383 Å °0.1548 Å °-0.1064 Å °0.0032 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:129)

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