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- PDB-6f1o: Orthorhombic Lysozyme crystallized at 298 K and pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 6f1o
TitleOrthorhombic Lysozyme crystallized at 298 K and pH 4.5
ComponentsLysozyme C
KeywordsHYDROLASE
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
PHOSPHATE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.96 Å
AuthorsCamara-Artigas, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78020-R Spain
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding.
Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Camara-Artigas, A.
History
DepositionNov 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4623
Polymers14,3311
Non-polymers1302
Water3,081171
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-10 kcal/mol
Surface area6350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.062, 56.176, 73.289
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.2 M Sodium Chloride, 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationMonochromator: CHANNEL-CUT MONOCHROMATOR AND A KIRKPATRICK-BAEZ (KB) FOCUSING SYSTEM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 0.96→18.73 Å / Num. obs: 76153 / % possible obs: 99.3 % / Redundancy: 10 % / Biso Wilson estimate: 10.975 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.017 / Rrim(I) all: 0.053 / Net I/σ(I): 23.1 / Num. measured all: 763574 / Scaling rejects: 76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
0.96-0.987.50.79133070.7450.2950.84888.4
5.26-18.739.20.0515020.9930.0180.05592.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E3U

4e3u


Resolution: 0.96→17.963 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0.37 / Phase error: 11.32
RfactorNum. reflection% reflection
Rfree0.1416 7263 5 %
Rwork0.1312 --
obs0.1317 76068 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 47.78 Å2 / Biso mean: 16.1177 Å2 / Biso min: 8.44 Å2
Refinement stepCycle: final / Resolution: 0.96→17.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 6 171 1158
Biso mean--25.28 26.53 -
Num. residues----127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.96-0.97090.25761990.23893877407683
0.9709-0.98230.24922460.2244539478598
0.9823-0.99430.21182920.2014586487899
0.9943-1.00690.17372880.186145684856100
1.0069-1.02010.18062620.162446174879100
1.0201-1.03410.17842590.159946304889100
1.0341-1.04890.17141980.145946334831100
1.0489-1.06450.14012590.135646654924100
1.0645-1.08120.1562720.138746194891100
1.0812-1.09890.14482110.122246754886100
1.0989-1.11780.12912490.116146424891100
1.1178-1.13820.1172810.110745444825100
1.1382-1.16010.12772280.103846614889100
1.1601-1.18370.11922360.101146454881100
1.1837-1.20950.1242770.145814858100
1.2095-1.23760.12892000.106946574857100
1.2376-1.26850.1212400.105246454885100
1.2685-1.30280.13352420.109646554897100
1.3028-1.34110.12242110.106946384849100
1.3411-1.38440.11352530.107446214874100
1.3844-1.43390.13722250.10546664891100
1.4339-1.49130.11722610.107746184879100
1.4913-1.55910.1191850.107746764861100
1.5591-1.64120.13482540.109746184872100
1.6412-1.7440.12712350.11646454880100
1.744-1.87850.15872550.130646504905100
1.8785-2.06730.15082470.132745874834100
2.0673-2.36590.13232280.131846514879100
2.3659-2.97860.15392460.143646184864100
2.9786-17.96660.14392240.15184561478598

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