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- PDB-1b1g: SOLVATED REFINEMENT OF CA-LOADED CALBINDIN D9K -

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Basic information

Entry
Database: PDB / ID: 1b1g
TitleSOLVATED REFINEMENT OF CA-LOADED CALBINDIN D9K
ComponentsPROTEIN (CALBINDIN D9K)
KeywordsMETAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN
Function / homology
Function and homology information


vitamin D binding / calcium-dependent protein binding / basolateral plasma membrane / apical plasma membrane / calcium ion binding / cytoplasm
Similarity search - Function
S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand domain / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand domain / EF-hand / Recoverin; domain 1 / 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 speciesBos taurus (domestic cattle)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MD WITH EXPLICIT SOLVENT
AuthorsKordel, J. / Pearlman, D.A. / Chazin, W.J.
Citation
Journal: J.Biomol.NMR / Year: 1997
Title: Protein solution structure calculations in solution: solvated molecular dynamics refinement of calbindin D9k.
Authors: Kordel, J. / Pearlman, D.A. / Chazin, W.J.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: High-Resolution Solution Structure of Calcium-Loaded Calbindin D9k
Authors: Kordel, J. / Skelton, N.J. / Akke, M. / Chazin, W.J.
#2: Journal: Biochemistry / Year: 1990
Title: The Rate and Structural Consequences of Proline Cis-Trans Isomerization in Calbindin D9k: NMR Studies of the Minor (Cis-Pro43) Isoform and the Pro43Gly Mutant
Authors: Kordel, J. / Forsen, S. / Drakenberg, T. / Chazin, W.J.
#3: Journal: Biochemistry / Year: 1989
Title: 1H NMR Sequential Resonance Assignments, Secondary Structure, and Global Fold in Solution of the Major (Trans-Pro43) Form of Bovine Calbindin D9k
Authors: Kordel, J. / Forsen, S. / Chazin, W.J.
#4: Journal: J.Biol.Chem. / Year: 1986
Title: The Refined Structure of Vitamin D-Dependent Calcium-Binding Protein from Bovine Intestine. Molecular Details, Ion Binding, and Implications for the Structure of Other Calcium-Binding Proteins
Authors: Szebenyi, D.M.E. / Moffat, K.
History
DepositionNov 20, 1998Processing site: NDB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details / Item: _pdbx_database_related.content_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CALBINDIN D9K)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5513
Polymers8,4701
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)10 / 10ALL CONFORMERS USED
Representative

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Components

#1: Protein PROTEIN (CALBINDIN D9K) / INTESTINAL CALCIUM-BINDING PROTEIN


Mass: 8470.492 Da / Num. of mol.: 1 / Mutation: P43G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P02633
#2: Chemical ChemComp-CA / CALCIUM ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: AUTHOR USED THE NMR DATA FROM ENTRY 2BCB.

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR software
NameVersionDeveloperClassification
Amber4D.A.PEARLMAN,D.A.CASE,J.C.CALDWELL,G.L.SEIBEL,U.C.SINGH,P.WEINER AND P.A.KOLLMANrefinement
DISGEO, AMBERstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MD WITH EXPLICIT SOLVENT
Software ordinal: 1
Details: PREVIOUSLY CALCULATED DISGEO STRUCTURES WERE PLACED IN A BATH OF WATER MOLECULES AND CALCIUM IONS WERE ADDED IN THE BINDING SITES. THE SYSTEM WAS ENERGY MINIMIZED TO REMOVE BAD CONTACTS, ...Details: PREVIOUSLY CALCULATED DISGEO STRUCTURES WERE PLACED IN A BATH OF WATER MOLECULES AND CALCIUM IONS WERE ADDED IN THE BINDING SITES. THE SYSTEM WAS ENERGY MINIMIZED TO REMOVE BAD CONTACTS, THEN ANNEALED AT 300 K. DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: ALL CONFORMERS USED / Conformers calculated total number: 10 / Conformers submitted total number: 10

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