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- PDB-8epv: 2.2 A crystal structure of the lipocalin cat allergen Fel d 7 -

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Basic information

Entry
Database: PDB / ID: 8epv
Title2.2 A crystal structure of the lipocalin cat allergen Fel d 7
ComponentsFel d 7 allergen
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 region / ACETATE ION / Fel d 7 allergen
Function and homology information
Biological speciesFelis catus (domestic cat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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

Downloads & links

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Assembly

Deposited unit
A: Fel d 7 allergen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2066
Polymers17,8881
Non-polymers3175
Water55831
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)85.871, 85.871, 40.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-204-

ZN

21A-315-

HOH

31A-328-

HOH

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

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Components

#1: Protein Fel d 7 allergen


Mass: 17888.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: LOC100533977 / Production host: Escherichia coli (E. coli) / References: UniProt: E5D2Z5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 35 % MPD, 100 mM cacodylate pH 6.5, and 0.05 M Zinc acetate

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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: Feb 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 8074 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 42.55 Å2 / CC1/2: 0.996 / Net I/σ(I): 22.4
Reflection shellResolution: 2.19→2.24 Å / Num. unique obs: 379 / CC1/2: 0.655

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Processing

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

Resolution: 2.19→38.4 Å / SU ML: 0.292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8261
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2649 402 5.02 %
Rwork0.2413 7605 -
obs0.2427 8007 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.4 Å2
Refinement stepCycle: LAST / Resolution: 2.19→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 0 11 31 1033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511013
X-RAY DIFFRACTIONf_angle_d0.72241370
X-RAY DIFFRACTIONf_chiral_restr0.0472162
X-RAY DIFFRACTIONf_plane_restr0.0054174
X-RAY DIFFRACTIONf_dihedral_angle_d12.1103353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.510.34781300.24822442X-RAY DIFFRACTION97.35
2.51-3.160.27751320.27692505X-RAY DIFFRACTION99.4
3.16-38.40.2471400.22822658X-RAY DIFFRACTION99.75
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)
19.3725814322.30921116441-1.450365342653.27548256319-1.520112184023.97619008709-0.102365787470.2197299436410.30844484370.353465493090.1506258587690.4505763535310.532211730995-0.2247915109750.02687739312610.4102847826120.0162323479212-0.01894778684870.176103221281-0.07459972621780.528426971199-5.76969171491-17.2860827668-1.61282831303
24.18144326271.83733111255-0.7044482463922.84319169383-1.251955926992.62412681187-0.452310629826-0.00492699268951-0.3168592466950.148257939984-0.109199898181-0.1323845940740.3766265730120.1846839806020.1988863325360.365685818995-0.104761406867-0.0650212692550.310601048815-0.01874393617710.611658565176-6.42737968511-23.1033222105-7.29617980586
33.66515523305-0.164650865456-2.990904071183.69541914253-1.303047019828.25988649060.2684508776670.665174979493-1.19034167466-0.2499520334980.20465095516-0.5493302615910.02144825666720.955134713640.5277884765310.415338800987-0.06259615240670.06378764547480.640277860709-0.1939779389140.616453689862-5.7777657927-26.9374359249-13.1152233116
42.191579965770.0102895019329-0.01058082299471.800780133080.7919430506322.637364859180.1083289851670.111298200939-0.9040326205890.521310326782-0.2920526106320.4271386463611.21442411874-0.429013838684-0.1691662302830.578364449298-0.361451871866-0.3284785272240.003116370853760.0992503740781.08327347126-6.72571785262-31.72162954025.61410758106
55.50117532975-0.3537634061352.079996459663.464829998641.329810394594.598504477250.150329746234-0.388850696113-0.2612604223970.4682833602740.05490624027440.241173705321-0.09225401560630.154260296319-0.08523305620980.280171091122-0.0405347415106-0.02627859508380.3520895560590.007227177280260.506951860514-1.77470004466-19.18780396555.85927388161
64.34049475147-2.726926323621.317906231936.364878094561.107650027343.416776043840.1662517737490.180553193009-0.7110404972090.4628921589120.147496151220.3135431871730.04532454243340.0329451254164-0.2224141988770.157460537064-0.0526534619526-0.0687252583120.240699785040.007582513270770.6263671798552.05450733429-23.76259639190.386559265493
73.5188603808-0.7577808479813.250205158332.5672525341.1004237234.85755608215-1.082819009430.2181887963530.801800032546-0.2046770112660.4565058019820.158809731669-0.4804813635010.5852547914850.3023640718790.383849083672-0.017909624932-0.08278666338190.1917127536770.08052571557660.563265224548-2.65557261396-8.1279906497-3.19307967291
85.27088614161-3.604317231892.995255873158.827898621380.09770292306045.36615189473-0.05056423755740.2726375029080.649492642141-0.0514641857011-0.253018932763-0.61600629816-0.5950355758250.620073676337-0.06223118424880.2321645540920.00876974865046-0.007441749353780.2413441278510.009773828864520.5645065223528.26515640569-14.46974245784.42850316246
94.05971639286-2.522885781461.872865857813.86916334745-1.594658768395.845897639750.1714817398241.50352180862-0.2768410471470.133453702059-0.2076083104090.0339450422545-0.4858575074561.24391608868-0.1090616025560.3516133029970.0476529066476-0.09682447696910.465830290278-0.07814707990030.5982621956735.8195656736-17.0784117269-8.34438377224
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 42 )27 - 421 - 16
22chain 'A' and (resid 43 through 75 )43 - 7517 - 45
33chain 'A' and (resid 76 through 86 )76 - 8646 - 56
44chain 'A' and (resid 87 through 101 )87 - 10157 - 71
55chain 'A' and (resid 102 through 113 )102 - 11372 - 83
66chain 'A' and (resid 114 through 135 )114 - 13584 - 101
77chain 'A' and (resid 136 through 141 )136 - 141102 - 107
88chain 'A' and (resid 142 through 155 )142 - 155108 - 121
99chain 'A' and (resid 156 through 170 )156 - 170122 - 136

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