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- PDB-2lap: NMR structure of Ca2+-bound CaBP1 C-domain with RDC -

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Basic information

Entry
Database: PDB / ID: 2lap
TitleNMR structure of Ca2+-bound CaBP1 C-domain with RDC
ComponentsCalcium-binding protein 1
KeywordsMETAL BINDING PROTEIN / EF-hand
Function / homology
Function and homology information


enzyme inhibitor activity / Sensory processing of sound by inner hair cells of the cochlea / response to stimulus / nuclear localization sequence binding / negative regulation of protein import into nucleus / calcium channel regulator activity / visual perception / calcium-dependent protein binding / cell cortex / postsynaptic density ...enzyme inhibitor activity / Sensory processing of sound by inner hair cells of the cochlea / response to stimulus / nuclear localization sequence binding / negative regulation of protein import into nucleus / calcium channel regulator activity / visual perception / calcium-dependent protein binding / cell cortex / postsynaptic density / cytoskeleton / Golgi membrane / calcium ion binding / perinuclear region of cytoplasm / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
Calcium binding protein 1/2/4/5 / 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 ...Calcium binding protein 1/2/4/5 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsAmes, J.
CitationJournal: To be Published
Title: 1H, 15N, and 13C chemical shift assignments for CaBP1 with 3 Ca2+ bound
Authors: Ames, J.
History
DepositionMar 16, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 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_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_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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 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: Calcium-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5373
Polymers19,4571
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)15 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calcium-binding protein 1 / / CaBP1 / Calbrain / Caldendrin


Mass: 19457.039 Da / Num. of mol.: 1 / Fragment: EF-hands 1-4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CABP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZU7
#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
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY

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Sample preparation

DetailsContents: 1.0 mM [U-98% 13C; U-98% 15N] CaBP1, 5.0 mM calcium, 10.0 mM TRIS, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMCaBP1-1[U-98% 13C; U-98% 15N]1
5.0 mMcalcium-21
10.0 mMTRIS-31
95 %H2O-41
5 %D2O-51
Sample conditionsIonic strength: 0.01 / pH: 7.4 / Pressure: ambient / Temperature: 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
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.23Schwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 15

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