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- PDB-4odd: Crystal structure of a dog lipocalin allergen -

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Basic information

Entry
Database: PDB / ID: 4odd
TitleCrystal structure of a dog lipocalin allergen
ComponentsLIPOCALIN ALLERGEN
KeywordsALLERGEN
Function / homology
Function and homology information


small molecule binding / extracellular region
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Can f 4 variant allergen
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNiemi, M.H. / Rouvinen, J.
CitationJournal: Mol.Immunol. / Year: 2014
Title: Structural aspects of dog allergies: The crystal structure of a dog dander allergen Can f 4.
Authors: Niemi, M.H. / Rytkonen-Nissinen, M. / Janis, J. / Virtanen, T. / Rouvinen, J.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: LIPOCALIN ALLERGEN
A: LIPOCALIN ALLERGEN
C: LIPOCALIN ALLERGEN


Theoretical massNumber of molelcules
Total (without water)52,9533
Polymers52,9533
Non-polymers00
Water0
1
B: LIPOCALIN ALLERGEN


Theoretical massNumber of molelcules
Total (without water)17,6511
Polymers17,6511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: LIPOCALIN ALLERGEN


Theoretical massNumber of molelcules
Total (without water)17,6511
Polymers17,6511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LIPOCALIN ALLERGEN


Theoretical massNumber of molelcules
Total (without water)17,6511
Polymers17,6511
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.600, 74.430, 167.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C and (resseq 12:44 or resseq 49:56 or resseq...
21chain A and (resseq 12:44 or resseq 49:56 or resseq...
31chain B and (resseq 12:44 or resseq 49:56 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain C and (resseq 12:44 or resseq 49:56 or resseq...C12 - 44
121chain C and (resseq 12:44 or resseq 49:56 or resseq...C49 - 56
131chain C and (resseq 12:44 or resseq 49:56 or resseq...C62 - 70
141chain C and (resseq 12:44 or resseq 49:56 or resseq...C84 - 91
151chain C and (resseq 12:44 or resseq 49:56 or resseq...C96 - 103
161chain C and (resseq 12:44 or resseq 49:56 or resseq...C111 - 119
171chain C and (resseq 12:44 or resseq 49:56 or resseq...C127 - 156
211chain A and (resseq 12:44 or resseq 49:56 or resseq...A12 - 44
221chain A and (resseq 12:44 or resseq 49:56 or resseq...A49 - 56
231chain A and (resseq 12:44 or resseq 49:56 or resseq...A62 - 70
241chain A and (resseq 12:44 or resseq 49:56 or resseq...A84 - 91
251chain A and (resseq 12:44 or resseq 49:56 or resseq...A96 - 103
261chain A and (resseq 12:44 or resseq 49:56 or resseq...A111 - 119
271chain A and (resseq 12:44 or resseq 49:56 or resseq...A127 - 156
311chain B and (resseq 12:44 or resseq 49:56 or resseq...B12 - 44
321chain B and (resseq 12:44 or resseq 49:56 or resseq...B49 - 56
331chain B and (resseq 12:44 or resseq 49:56 or resseq...B62 - 70
341chain B and (resseq 12:44 or resseq 49:56 or resseq...B84 - 87
351chain B and (resseq 12:44 or resseq 49:56 or resseq...B96 - 103
361chain B and (resseq 12:44 or resseq 49:56 or resseq...B111 - 119
371chain B and (resseq 12:44 or resseq 49:56 or resseq...B127 - 156

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Components

#1: Protein LIPOCALIN ALLERGEN


Mass: 17651.107 Da / Num. of mol.: 3 / Fragment: UNP residues 17-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: OBP / Production host: Pichia pastoris (fungus) / References: UniProt: J9P950

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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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% PEG 8000, 0.2M potassium phosphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→44.6 Å / Num. all: 15956 / Num. obs: 15857 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 52.68 Å2 / Rsym value: 0.042 / Net I/σ(I): 23.42
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1665 / Rsym value: 0.331 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.14data extraction
DNAdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.6 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 2.01 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2806 793 5 %RANDOM
Rwork0.2373 ---
obs0.2394 15850 99.35 %-
all-15857 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.496 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 177.79 Å2 / Biso mean: 59.6897 Å2 / Biso min: 20.25 Å2
Baniso -1Baniso -2Baniso -3
1-16.4049 Å2-0 Å2-0 Å2
2---6.0958 Å20 Å2
3----10.309 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 0 0 3527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093593
X-RAY DIFFRACTIONf_angle_d1.2454843
X-RAY DIFFRACTIONf_chiral_restr0.076527
X-RAY DIFFRACTIONf_plane_restr0.004636
X-RAY DIFFRACTIONf_dihedral_angle_d15.6861359
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C831X-RAY DIFFRACTIONPOSITIONAL0.058
12A831X-RAY DIFFRACTIONPOSITIONAL0.058
13B796X-RAY DIFFRACTIONPOSITIONAL0.06
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.7630.38981290.32262458258799
2.763-2.97630.35161300.291424612591100
2.9763-3.27580.31121300.25142469259999
3.2758-3.74960.30581310.24624952626100
3.7496-4.72320.27191320.2112507263999
4.7232-44.64450.22521410.21982667280899

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