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- PDB-4r0p: Ifqins, an amyloid forming segment from human lysozyme spanning r... -

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Basic information

Entry
Database: PDB / ID: 4r0p
TitleIfqins, an amyloid forming segment from human lysozyme spanning residues 56-61
ComponentsLysozyme C
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
Function / homology
Function and homology information


antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.52 Å
AuthorsSievers, S. / Eisenberg, D.S. / Sawaya, M.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Structure-based design of functional amyloid materials.
Authors: Li, D. / Jones, E.M. / Sawaya, M.R. / Furukawa, H. / Luo, F. / Ivanova, M. / Sievers, S.A. / Wang, W. / Yaghi, O.M. / Liu, C. / Eisenberg, D.S.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 C


Theoretical massNumber of molelcules
Total (without water)7211
Polymers7211
Non-polymers00
Water362
1
A: Lysozyme C
x 10


Theoretical massNumber of molelcules
Total (without water)7,20810
Polymers7,20810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation3_454-x-1,y+1/2,-z-1/21
crystal symmetry operation3_434-x-1,y-3/2,-z-1/21
crystal symmetry operation3_444-x-1,y-1/2,-z-1/21
crystal symmetry operation3_464-x-1,y+3/2,-z-1/21
crystal symmetry operation3_474-x-1,y+5/2,-z-1/21
Unit cell
Length a, b, c (Å)19.607, 4.839, 43.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThere are two choices of the biological unit (fibrils). The first choice is a pair of indefinitely long beta sheets constructed from chain A and unit cell translations along the b direction (the b direction corresponds to the fiber axis) (i.e. X,Y,Z; X,Y+1,Z; X,Y+2,Z; etc.) together with a symmetry related sheet formed from -X,1/2+Y,-1/2-Z and its unit cell translations along the b direction (i.e. -X,3/2+Y,-1/2-Z; -X,5/2+Y,-1/2-Z, etc.). The second choice of biological unit is a pair of beta sheets constructed from chain A and unit cell translations along the b direction (i.e. X,Y,Z; X,Y+1,Z; X,Y+2,Z; etc.) together with a symmetry related sheet formed from -1-X,1/2+Y,-1/2-Z and its unit cell translations along the b direction (i.e. -1-X,3/2+Y,-1/2-Z; -1-X,5/2+Y,-1/2-Z, etc.). REMARK 350 displays 5 strands from both sheets for the second choice.

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Components

#1: Protein/peptide Lysozyme C / 1 / 4-beta-N-acetylmuramidase C


Mass: 720.814 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 74-79 / Source method: obtained synthetically
Details: IFQINS hexapeptide (residues 56-61) from human lysozyme, synthesized
Source: (synth.) Homo sapiens (human) / References: UniProt: P61626, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 1.42 Å3/Da / Density % sol: 13.51 % / Mosaicity: 0.3 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: reservoir contained 0.1M Bis-Tris pH 6.5, 3.0M Sodium Chloride, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. all: 753 / Num. obs: 753 / % possible obs: 93.8 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.181 / Χ2: 1.055 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.628.80.4221281.07881
1.62-1.789.70.3781291.01494.2
1.78-2.0416.40.2421461.05496.7
2.04-2.5615.70.1961631.09296.4
2.56-9013.80.1251871.02899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.31 Å21.61 Å
Translation2.31 Å21.61 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→21.61 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1884 / WRfactor Rwork: 0.1458 / FOM work R set: 0.8701 / SU B: 1.566 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0948 / SU Rfree: 0.0969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 77 10.5 %RANDOM
Rwork0.1578 ---
all0.1623 ---
obs0.1623 732 92.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 20.85 Å2 / Biso mean: 4.924 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.52→21.61 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms51 0 0 2 53
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02357
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.94478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50326.6673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.7211511
X-RAY DIFFRACTIONr_chiral_restr0.1290.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0243
X-RAY DIFFRACTIONr_nbd_refined0.2080.210
X-RAY DIFFRACTIONr_nbtor_refined0.3240.237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.10.28
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.010.21
X-RAY DIFFRACTIONr_mcbond_it1.435236
X-RAY DIFFRACTIONr_mcangle_it2.474356
X-RAY DIFFRACTIONr_scbond_it2.129225
X-RAY DIFFRACTIONr_scangle_it2.005321
LS refinement shellResolution: 1.524→1.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 7 -
Rwork0.215 36 -
all-43 -
obs--75.44 %

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