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- PDB-2mbx: Structure, dynamics and stability of allergen cod parvalbumin Gad... -

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Basic information

Entry
Database: PDB / ID: 2mbx
TitleStructure, dynamics and stability of allergen cod parvalbumin Gad m 1 by solution and high-pressure NMR.
ComponentsParvalbumin beta
KeywordsCONTRACTILE PROTEIN / Allergen / Parvalbumin / EF-hand
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Parvalbumin / 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 ...Parvalbumin / 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 speciesGadus morhua (Atlantic cod)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsMoraes, A.H. / Ackerbauer, D. / Bublin, M. / Ferreira, F. / Almeida, F.C.L. / Breiteneder, H. / Valente, A.
Citation
Journal: Proteins / Year: 2014
Title: Solution and high-pressure NMR studies of the structure, dynamics, and stability of the cross-reactive allergenic cod parvalbumin Gad m 1.
Authors: Moraes, A.H. / Ackerbauer, D. / Kostadinova, M. / Bublin, M. / de Oliveira, G.A. / Ferreira, F. / Almeida, F.C. / Breiteneder, H. / Valente, A.P.
#1: Journal: Biomol.Nmr Assign. / Year: 2013
Title: (1)H, (13)C and (15)N resonance assignments and second structure information of Gad m 1: a beta-parvalbumin allergen from Atlantic cod (Gadus morhua).
Authors: Moraes, A.H. / Ackerbauer, D. / Kostadinova, M. / Bublin, M. / Ferreira, F. / Almeida, F.C. / Breiteneder, H. / Valente, A.P.
History
DepositionAug 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parvalbumin beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6453
Polymers11,5651
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Parvalbumin beta


Mass: 11565.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gadus morhua (Atlantic cod) / Production host: Gadus morhua (Atlantic cod) / References: UniProt: Q90YK9
#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 1H-15N HSQC NH2 only
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D HN(CO)CA
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic
11313D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 0.6-1.0 uM [U-100% 13C; U-100% 15N] Gad m 1, 10 mM sodium phosphate, 0.5 mM calcium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMGad m 1-1[U-100% 13C; U-100% 15N]0.6-1.01
10 mMsodium phosphate-21
0.5 mMcalcium chloride-31
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TALOS+Yang Shenstructure solution
CARA1.8.4Rochus Kellerchemical shift assignment
CNSrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1505
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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