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- PDB-1h4b: SOLUTION STRUCTURE OF THE BIRCH POLLEN ALLERGEN BET V 4 -

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Basic information

Entry
Database: PDB / ID: 1h4b
TitleSOLUTION STRUCTURE OF THE BIRCH POLLEN ALLERGEN BET V 4
ComponentsPOLCALCIN BET V 4
KeywordsALLERGEN / BIRCH POLLEN ALLERGEN / CALCIUM-BINDING POLCALCIN / HETERONUCLEAR NMR
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
: / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain ...: / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBETULA VERRUCOSA (European white birch)
MethodSOLUTION NMR / simulated annealing
AuthorsNeudecker, P. / Nerkamp, J. / Eisenmann, A. / Lauber, T. / Lehmann, K. / Schweimer, K. / Roesch, P.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution Structure, Dynamics, and Hydrodynamics of the Calcium-Bound Cross-Reactive Birch Pollen Allergen Bet V 4 Reveal a Canonical Monomeric Two EF-Hand Assembly with a Regulatory Function
Authors: Neudecker, P. / Nerkamp, J. / Eisenmann, A. / Nourse, A. / Lauber, T. / Schweimer, K. / Lehmann, K. / Schwarzinger, S. / Ferreira, F. / Roesch, P.
History
DepositionFeb 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLCALCIN BET V 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4113
Polymers9,3301
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 90LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein POLCALCIN BET V 4 / CALCIUM-BINDING POLLEN ALLERGEN BET V 4


Mass: 9330.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BETULA VERRUCOSA (European white birch)
Plasmid: PMW175 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q39419
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-TOCSY
1212D-NOESY
1311H
14115N-HSQC
1511H
16115N-IPAP
171HNHA
1813D-1H
19115N-TOCSY-HSQC
11013D-1H
111115N/1H
112115N- HMQC-NOESY-HSQC
11313D-1H
114113C/1H
115115N- HMQC-NOESY-HSQC
116113C-CTHSQC
1171HNCO
1181LONG-RANGE H(N)CO
1191C(CO)NH
1201HNCA
1211H(C)CH-COSY
1221(H)CCH-COSY
12313D-1H
124113C-NOESY-HSQC

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Sample preparation

Sample conditionsIonic strength: 45 mM / pH: 6 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DMXBrukerDMX7502

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH1.2.1BRUNGER, CLORE, KUSZEWSKI, SCHWIETERS, TJrefinement
NDEEstructure solution
NMRView5.0.4structure solution
Xplor-NIH1.2.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 90 / Conformers submitted total number: 25

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