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- PDB-6nre: Monomeric Lipocalin Can F 6 -

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Basic information

Entry
Database: PDB / ID: 6nre
TitleMonomeric Lipocalin Can F 6
ComponentsLipocalin-Can f 6 allergen
KeywordsALLERGEN / Lipocalin / metabolic role
Function / homology
Function and homology information


odorant binding / small molecule binding / extracellular space / extracellular region
Similarity search - Function
Major urinary protein / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Lipocalin Can f 6.0101
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsClayton G, M. / Kappler J, W. / Chan, S.
CitationJournal: Plos One / Year: 2019
Title: Structural characteristics of lipocalin allergens: Crystal structure of the immunogenic dog allergen Can f 6.
Authors: Clayton, G.M. / White, J. / Lee, S. / Kappler, J.W. / Chan, S.K.
History
DepositionJan 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Lipocalin-Can f 6 allergen


Theoretical massNumber of molelcules
Total (without water)21,0471
Polymers21,0471
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.154, 67.154, 72.488
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Lipocalin-Can f 6 allergen


Mass: 21046.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: lcn / Production host: Escherichia coli (E. coli) / References: UniProt: H2B3G5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2-propanol, sodium acetate, polyethylene glycol ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.06→72.49 Å / Num. obs: 12122 / % possible obs: 99.4 % / Redundancy: 17 % / CC1/2: 0.985 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.012 / Rrim(I) all: 0.052 / Net I/σ(I): 38.8 / Num. measured all: 69256 / Scaling rejects: 94
Reflection shellResolution: 2.06→2.11 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.3 / Num. measured all: 5492 / Num. unique obs: 872 / Rpim(I) all: 0.194 / Rrim(I) all: 0.457 / Net I/σ(I) obs: 0.1 / % possible all: 93

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→58.16 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 31.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1063 4.72 %
Rwork0.221 --
obs0.223 22536 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→58.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 0 13 1253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041275
X-RAY DIFFRACTIONf_angle_d0.6721723
X-RAY DIFFRACTIONf_dihedral_angle_d15.795773
X-RAY DIFFRACTIONf_chiral_restr0.051198
X-RAY DIFFRACTIONf_plane_restr0.003219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0567-2.15030.39541430.33452544X-RAY DIFFRACTION94
2.1503-2.26370.30241020.29132709X-RAY DIFFRACTION99
2.2637-2.40550.29221680.27912687X-RAY DIFFRACTION100
2.4055-2.59120.35051400.28432711X-RAY DIFFRACTION100
2.5912-2.8520.37631100.27142687X-RAY DIFFRACTION100
2.852-3.26470.27791500.25262694X-RAY DIFFRACTION100
3.2647-4.1130.21941330.20762714X-RAY DIFFRACTION100
4.113-58.180.20841170.18792727X-RAY DIFFRACTION100

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