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- PDB-1rjv: Solution Structure of Human alpha-Parvalbumin refined with a para... -

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Basic information

Entry
Database: PDB / ID: 1rjv
TitleSolution Structure of Human alpha-Parvalbumin refined with a paramagnetism-based strategy
ComponentsParvalbumin alpha
KeywordsMETAL BINDING PROTEIN / calcium / parvalbumin / EF-hand / lanthanide / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


inhibitory chemical synaptic transmission / excitatory chemical synaptic transmission / Transcriptional Regulation by MECP2 / gene expression / axon / calcium ion binding / synapse / cytoplasm
Similarity search - Function
Parvalbumin / 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 ...Parvalbumin / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics, pseudocontact shifts, residual dipolar coupling
AuthorsBaig, I. / Bertini, I. / Del Bianco, C. / Gupta, Y.K. / Lee, Y.M. / Luchinat, C. / Quattrone, A. / Structural Proteomics in Europe (SPINE)
CitationJournal: Biochemistry / Year: 2004
Title: Paramagnetism-Based Refinement Strategy for the Solution Structure of Human alpha-Parvalbumin.
Authors: Baig, I. / Bertini, I. / Del Bianco, C. / Gupta, Y.K. / Lee, Y.M. / Luchinat, C. / Quattrone, A.
History
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parvalbumin alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1583
Polymers12,0781
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)19 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Parvalbumin alpha


Mass: 12077.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVALB / Plasmid: pQE-30 Xa / Production host: Escherichia coli (E. coli) / References: UniProt: P20472
#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
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1312D NOESY
1412D TOCSY
NMR detailsText: This structure was determined using diamagnetic, Pseudocontact Shift and Residual dipolar coupling constraints

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM Parvalbumin U-15N,13C; 100mM NaCl; 90% H2O, 10% D2O; pH 7; for CaCaPV90% H2O/10% D2O
20.6mM Parvalbumin U-15N; 100mM NaCl; 90% H2O, 10% D2O; pH 7; for CaCaPV90% H2O/10% D2O
31.5mM Parvalbumin U-15N,13C; 100mM NaCl; 90% H2O, 10% D2O; pH 7; for CaDyPV90% H2O/10% D2O
40.6mM Parvalbumin U-15N; 100mM NaCl; 90% H2O, 10% D2O; pH 7; for CaDyPV90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 7ambient 298 K
2100 mM NaCl 7ambient 298 K
3100 mM NaCl 7ambient 298 K
4100 mM NaCl 7ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE5002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1BRUNGERcollection
XwinNMR3.1BRUNGERprocessing
XEASY1.3Guntertdata analysis
DYANA1.5Guntertstructure solution
Amber5Pearlmanrefinement
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics, pseudocontact shifts, residual dipolar coupling
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 19

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