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- PDB-2m28: NMR structure of Ca2+ bound CaBP4 C-domain -

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Basic information

Entry
Database: PDB / ID: 2m28
TitleNMR structure of Ca2+ bound CaBP4 C-domain
ComponentsCalcium-binding protein 4
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


retinal bipolar neuron differentiation / photoreceptor cell morphogenesis / retinal cone cell development / calcium channel regulator activity / phototransduction / visual perception / cell projection / presynapse / transmembrane transporter binding / calcium ion binding ...retinal bipolar neuron differentiation / photoreceptor cell morphogenesis / retinal cone cell development / calcium channel regulator activity / phototransduction / visual perception / cell projection / presynapse / transmembrane transporter binding / calcium ion binding / cytosol / cytoplasm
Similarity search - Function
Calcium binding protein 1/2/4/5 / EF hand / 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 ...Calcium binding protein 1/2/4/5 / EF hand / 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
Calcium-binding protein 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsAmes, J.B.
CitationJournal: To be Published
Title: Chemical shift assignment of Ca2+ bound CaPB4
Authors: Ames, J.
History
DepositionDec 17, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Other
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7273
Polymers19,6471
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)14 / 70structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calcium-binding protein 4 / CaBP4


Mass: 19647.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cabp4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VHC5
#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
2122D 1H-15N HSQC
3233D HNCO
3333D HN(CA)CO
141TROSY HN(CA)CB
151TROSY HN(CO)CACB
2633D (H)CCH-TOCSY
4742D 1H-1H COSY
4842D 1H-1H NOESY
59513C CT-HSQC
31033D 1H-15N NOESY
31133D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N; U-2H] CaBP4, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-15N] CaBP4, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-13C; U-15N] CaBP4, 90% H2O/10% D2O90% H2O/10% D2O
40.5 mM CaBP4, 90% H2O/10% D2O90% H2O/10% D2O
50.5 mM [U-10% 13C; U-99% 15N] CaBP4, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCaBP4-1[U-13C; U-15N; U-2H]1
0.5 mMCaBP4-2[U-15N]2
0.5 mMCaBP4-3[U-13C; U-15N]3
0.5 mMCaBP4-44
0.5 mMCaBP4-5[U-10% 13C; U-99% 15N]5
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.4 ambient 310 K
27.4 ambient 310 K
37.4 ambient 310 K
47.4 ambient 310 K
57.4 ambient 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 70 / Conformers submitted total number: 14

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