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- PDB-8epu: 1.6 A crystal structure of the lipocalin dog allergen Can f 1 wit... -

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Basic information

Entry
Database: PDB / ID: 8epu
Title1.6 A crystal structure of the lipocalin dog allergen Can f 1 with the C118S mutation
ComponentsMajor allergen Can f 1
KeywordsALLERGEN / Lipocalin / Fatty acid binding protein / Calyx
Function / homologyvon Ebner's gland protein/ Bos/Can allergen / Lipocalin / small molecule binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / extracellular space / Major allergen Can f 1
Function and homology information
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMin, J. / Pedersen, L.C. / Geoffrey, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Front Allergy / Year: 2023
Title: Structural and ligand binding analysis of the pet allergens Can f 1 and Fel d 7.
Authors: Min, J. / Foo, A.C.Y. / Gabel, S.A. / Perera, L. / DeRose, E.F. / Pomes, A. / Pedersen, L.C. / Mueller, G.A.
History
DepositionOct 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major allergen Can f 1


Theoretical massNumber of molelcules
Total (without water)16,5701
Polymers16,5701
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.214, 36.512, 57.973
Angle α, β, γ (deg.)90.000, 100.800, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-263-

HOH

DetailsThe oligomeric state is unknown. Lipocalin proteins are often in a transient monomer to oligomer state.

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Components

#1: Protein Major allergen Can f 1 / Allergen Dog 1


Mass: 16569.699 Da / Num. of mol.: 1 / Mutation: C118S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Production host: Escherichia coli (E. coli) / References: UniProt: O18873
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 35 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 16064 / % possible obs: 94 % / Redundancy: 3.1 % / Biso Wilson estimate: 24.85 Å2 / CC1/2: 0.986 / Net I/σ(I): 25.98
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 684 / CC1/2: 0.975

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Processing

Software
NameVersionClassification
SERGUI1.20.1_4487data collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 1.6→31.34 Å / SU ML: 0.1854 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 29.3045
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 802 5.01 %
Rwork0.2108 15193 -
obs0.2117 15995 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.43 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 0 68 1121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921126
X-RAY DIFFRACTIONf_angle_d1.02011540
X-RAY DIFFRACTIONf_chiral_restr0.058181
X-RAY DIFFRACTIONf_plane_restr0.0079200
X-RAY DIFFRACTIONf_dihedral_angle_d11.7318407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.70.32581210.27242302X-RAY DIFFRACTION84.87
1.7-1.830.29721320.25052489X-RAY DIFFRACTION93.27
1.83-2.010.28721390.22252626X-RAY DIFFRACTION97.19
2.01-2.310.25671370.21152618X-RAY DIFFRACTION97.59
2.31-2.910.22161370.23442600X-RAY DIFFRACTION95.53
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9309576345730.11528381324-1.222753905413.10254582945-0.4854515760281.647153382770.05324142914040.400333498627-0.0778739496202-0.102800322273-0.02514817029350.01440673226580.1372814027140.363447193997-0.03450992787120.2043295700180.033519469428-0.02650324232480.510634288470.01213062144950.136135807437-11.37588071055.5350342339215.8451805224
26.75806266984-1.58077446994-1.751044899221.87662004199-0.7443291161381.336160802360.05943881059870.0328004446308-0.349931335675-0.0906352937799-0.06321761974580.03982015871370.2745464946360.2106157435060.004524007470450.2570596204380.062567001898-0.02644147287110.320475349567-0.02672373876710.144957243166-8.10396278513-3.4584954269515.8190134268
31.76656672819-0.234262822618-0.405953677312.279100746770.4905857550445.7576209830.1375074310050.161868391450.0285560738595-0.06431045129330.0520477301874-0.00531382671980.1984207313830.0252655706551-0.1549679352490.192185470910.0342978968023-0.03473297945030.4246662050290.02687934824360.124159871121-4.752415174979.3987285672412.100879333
43.783430791551.1343797459-3.815160204232.42370828023-0.03779877769074.438632549120.042955249257-0.001181274058720.215024711942-0.0488637203565-0.08215859578190.3219153617080.1697045862620.3873205629370.04963896704240.219259621170.0638223195726-0.019726010570.576732591650.05107388960850.243214809004-15.94488630288.5138557616113.194126047
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 55 )27 - 551 - 29
22chain 'A' and (resid 56 through 100 )56 - 10030 - 74
33chain 'A' and (resid 101 through 153 )101 - 15375 - 127
44chain 'A' and (resid 154 through 171 )154 - 171128 - 145

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