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- PDB-1puo: Crystal structure of Fel d 1- the major cat allergen -

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Basic information

Entry
Database: PDB / ID: 1puo
TitleCrystal structure of Fel d 1- the major cat allergen
ComponentsMajor allergen I polypeptide, fused chain 2, chain 1
KeywordsALLERGEN / cat allergen / uteroglobin / secretoglobin
Function / homology
Function and homology information


steroid binding / extracellular space / extracellular region
Similarity search - Function
Histone Acetyltransferase; Chain A - #50 / Major allergen I polypeptide chain 1 / Major allergen I polypeptide chain 2-like / Allergen Fel d I-B chain / Uteroglobin / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Secretoglobin superfamily / Histone Acetyltransferase; Chain A ...Histone Acetyltransferase; Chain A - #50 / Major allergen I polypeptide chain 1 / Major allergen I polypeptide chain 2-like / Allergen Fel d I-B chain / Uteroglobin / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Secretoglobin superfamily / Histone Acetyltransferase; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Major allergen I polypeptide chain 1 / Major allergen I polypeptide chain 2
Similarity search - Component
Biological speciesFelis catus (domestic cat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKaiser, L. / Gronlund, H. / Sandalova, T. / Ljunggren, H.G. / van Hage-Hamsten, M. / Achour, A. / Schneider, G.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: The crystal structure of the major cat allergen Fel d 1, a member of the secretoglobin family.
Authors: Kaiser, L. / Gronlund, H. / Sandalova, T. / Ljunggren, H.G. / van Hage-Hamsten, M. / Achour, A. / Schneider, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Production, crystallization and preliminary crystallographic study of the major cat allergen Fel d 1.
Authors: Kaiser, L. / Gronlund, H. / Sandalova, T. / Ljunggren, H.G. / Schneider, G. / Van Hage-Hamsten, M. / Achour, A.
History
DepositionJun 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 3, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_biol
Item: _struct_biol.details
Remark 999SEQUENCE recombinant protein is fusion of mature chain 2 and chain 1 of Fel d 1
Remark 350GENERATING THE BIOMOLECULE THE BIOLOGICAL UNIT IS A DIMER. COORDINATES FOR A COMPLETE MULTIMER ...GENERATING THE BIOMOLECULE THE BIOLOGICAL UNIT IS A DIMER. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN NOT BE GENERATED BY APPLYING NEITHER NON-CRYSTALLOGRAPHIC NOR CRYSTALLOGRAPHIC OPERATIONS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major allergen I polypeptide, fused chain 2, chain 1
B: Major allergen I polypeptide, fused chain 2, chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6226
Polymers38,1502
Non-polymers4734
Water4,197233
1
A: Major allergen I polypeptide, fused chain 2, chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3113
Polymers19,0751
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Major allergen I polypeptide, fused chain 2, chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3113
Polymers19,0751
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.290, 51.539, 67.725
Angle α, β, γ (deg.)90.00, 95.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRCYSAA6 - 736 - 73
21THRCYSBB6 - 736 - 73
32GLUTYRAA93 - 12093 - 120
42GLUTYRBB93 - 12093 - 120
53GLUGLUAA128 - 164128 - 164
63GLUGLUBB128 - 164128 - 164
DetailsThe biological molecule is heterotetramer. The recombinant molecule is covalently fused heterodimer. Recombinant Fel d 1 does not form dimers in the crystal.

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Components

#1: Protein Major allergen I polypeptide, fused chain 2, chain 1 / Allergen Fel d 1-B / Allergen Fel d 1-A


Mass: 19074.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: CH2, CH1 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLys S / References: UniProt: P30440, UniProt: P30438
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 1.97 Å3/Da / Density % sol: 37.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: MPD, sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.5 mg/mlprotein1drop
220 mMTris-HCl1reservoirpH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMAX II I71111.13
SYNCHROTRONESRF ID2920.979
Detector
TypeIDDetectorDate
MARRESEARCH1CCDSep 14, 2002
ADSC QUANTUM 42CCDNov 21, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) monochromator crystalSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.131
20.9791
ReflectionResolution: 1.85→24.5 Å / Num. obs: 25173 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.089 / Net I/σ(I): 9.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 3511 / Rsym value: 0.46 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 69889 / Num. measured all: 25113 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.46

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→24.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.368 / SU ML: 0.103 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23731 1298 5.1 %RANDOM
Rwork0.20087 ---
all0.2027 ---
obs0.20275 24247 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.598 Å2
Baniso -1Baniso -2Baniso -3
1-2.34 Å20 Å20.01 Å2
2---0.96 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2202 0 0 265 2467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222262
X-RAY DIFFRACTIONr_bond_other_d0.0020.022115
X-RAY DIFFRACTIONr_angle_refined_deg1.2682.0143072
X-RAY DIFFRACTIONr_angle_other_deg0.834949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9915279
X-RAY DIFFRACTIONr_chiral_restr0.0710.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022413
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02379
X-RAY DIFFRACTIONr_nbd_refined0.2060.2623
X-RAY DIFFRACTIONr_nbd_other0.2220.22515
X-RAY DIFFRACTIONr_nbtor_other0.0840.21357
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1660.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.229
X-RAY DIFFRACTIONr_mcbond_it0.651.51415
X-RAY DIFFRACTIONr_mcangle_it1.23622304
X-RAY DIFFRACTIONr_scbond_it1.8973847
X-RAY DIFFRACTIONr_scangle_it3.2334.5768
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
788tight positional0.020.05
1211loose positional0.395
788tight thermal0.070.5
1211loose thermal0.4410
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 94 -
Rwork0.221 1782 -
obs-1782 99.7 %
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.27
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / Rfactor Rwork: 0.226

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