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- PDB-2ejn: Structural characterization of the tetrameric form of the major c... -

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Basic information

Entry
Database: PDB / ID: 2ejn
TitleStructural characterization of the tetrameric form of the major cat allergen fel D 1
ComponentsMajor allergen I polypeptide chain 1, chain 2
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 / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Uteroglobin / Secretoglobin superfamily ...Histone Acetyltransferase; Chain A - #50 / Major allergen I polypeptide chain 1 / Major allergen I polypeptide chain 2-like / : / Allergen Fel d I-B chain / Secretoglobin / Uteroglobin family / Secretoglobin (SCGB) family profile. / Uteroglobin / 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 / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsKaiser, L. / Velickovic, T.C. / Badia-Martinez, D. / Adedoyin, J. / Thunberg, S. / Hallen, D. / Berndt, K. / Gronlund, H. / Gafvelin, G. / van Hage, M. / Achour, A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural characterization of the tetrameric form of the major cat allergen Fel d 1
Authors: Kaiser, L. / Velickovic, T.C. / Badia-Martinez, D. / Adedoyin, J. / Thunberg, S. / Hallen, D. / Berndt, K. / Gronlund, H. / Gafvelin, G. / van Hage, M. / Achour, A.
History
DepositionMar 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,5786
Polymers34,4182
Non-polymers1604
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-50 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.588, 42.996, 48.906
Angle α, β, γ (deg.)70.80, 80.56, 81.53
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17208.809 Da / Num. of mol.: 2
Fragment: MATURE CHAIN 1 and residues of CHAIN 2 in database 18-93
Source method: isolated from a genetically manipulated source
Details: Biochemical fusion of chain 1 and chain 2 of Fel d 1
Source: (gene. exp.) Felis catus (domestic cat) / Gene: ch1, ch2 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P30438, UniProt: P30440
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22.5% PEG3350, 0.5M CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.087 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2004
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 1.64→36.51 Å / Num. obs: 31695 / % possible obs: 92.93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUO

1puo


Resolution: 1.64→36.51 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1680 -RANDOM
Rwork0.19 ---
obs0.19 31695 92.93 %-
Refinement stepCycle: LAST / Resolution: 1.64→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 4 270 2533

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