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- PDB-1d1o: COOPERATIVITY IN EF-HAND CA2+-BINDING PROTEINS: EVIDENCE OF SITE-... -

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Basic information

Entry
Database: PDB / ID: 1d1o
TitleCOOPERATIVITY IN EF-HAND CA2+-BINDING PROTEINS: EVIDENCE OF SITE-SITE COMMUNICATION FROM BINDING-INDUCED CHANGES IN STRUCTURE AND DYNAMICS OF N56A CALBINDIN D9K
ComponentsCALBINDIN D9K
KeywordsSIGNALING PROTEIN / EF-HAND / CALCIUM-BINDING PROTEIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


vitamin D binding / calcium-dependent protein binding / collagen-containing extracellular matrix / calcium ion binding / extracellular space / 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 / 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 / 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 (cattle)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsMaler, L. / Blankenship, J. / Rance, M. / Chazin, W.J.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Site-site communication in the EF-hand Ca2+-binding protein calbindin D9k.
Authors: Maler, L. / Blankenship, J. / Rance, M. / Chazin, W.J.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Solution structure of (cd2+)1-calbindin D9k reveals details of the stepwise structural changes along the apo-(Ca2+)1-(Ca2+)2 binding pathway.
Authors: Akke, M. / Forsen, S. / Chazin, W.J.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: Determination of the solution structure of apo calbindin D9k by NMR spectroscopy.
Authors: Skelton, N.J. / Kordel, J. / Chazin, W.J.
#4: Journal: Protein Sci. / Year: 1995
Title: Characterization of the N-terminal half-saturated state of calbindin D9k: NMR studies of the N56A mutant.
Authors: Wimberly, B. / Thulin, E. / Chazin, W.J.
History
DepositionSep 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
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: CALBINDIN D9K


Theoretical massNumber of molelcules
Total (without water)8,5021
Polymers8,5021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 50STRUCTURES WITH ACCEPTABLE MOLECULAR ENEGIES WERE ORDERED BY LEAST RESTRAINT VIOLATIONS. THE 24 BEST CONFORMERS WERE SELECTED TO FACILITATE COMPARISON TO PREVIOUS STRUCTURES OF THE PROTEIN AND BECAUSE THIS SURPASSES THE STATISTICAL REQUIREMENT TO REPRESENT ALL OF CONFORMATIONAL SPACE CONSISTENT WITH THE DATA.
RepresentativeModel #1closest to the average

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Components

#1: Protein CALBINDIN D9K


Mass: 8501.611 Da / Num. of mol.: 1 / Fragment: CALBINDIN D9K / Mutation: P43M, N56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P02633

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2223D 15N-SEPARATED NOESY
232HSQC-J
NMR detailsText: 1H RESONANCE ASIGNMENTS WERE REPORTED IN THE PROTEIN SCIENCE PAPER BY WIMBERLY ET AL. A 3D 15N SPARATED TOCSY WAS RECORDED TO CONFIRM THESE ASSIGNMENTS AND ASSIGN THE 15N RESONANCES.

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Sample preparation

Details
Solution-IDContents
14 MM N56A-CALBINDIN D9K
24 MM 15N-LABELED N56A-CALBINDIN D9K;
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 6.0 AMBIENT 300 K
20 6.0 AMBIENT 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
Felix97MSI, SAN DIEGO, CAstructure solution
DIANA2.8GUNTERT, BRAUN, BILLETER, WUTHRICHstructure solution
Amber4.1PEARLMAN, CASE, CALDWELL, ROSS, CHEATHAM, FERGUSON, SEIBEL, SINGH, WEINER, KOLLMANrefinement
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: NMR REFINEMENT WAS BASED ON A TOTAL OF 910 NOE-DERIVED DISTANCE CONSTRAINTS AND 78 TORSION ANGLE CONSTRAINTS. SIMULATED ANNEALING CYCLE OF 20 PS HEATING TO 1200 K.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE MOLECULAR ENEGIES WERE ORDERED BY LEAST RESTRAINT VIOLATIONS. THE 24 BEST CONFORMERS WERE SELECTED TO FACILITATE COMPARISON TO PREVIOUS ...Conformer selection criteria: STRUCTURES WITH ACCEPTABLE MOLECULAR ENEGIES WERE ORDERED BY LEAST RESTRAINT VIOLATIONS. THE 24 BEST CONFORMERS WERE SELECTED TO FACILITATE COMPARISON TO PREVIOUS STRUCTURES OF THE PROTEIN AND BECAUSE THIS SURPASSES THE STATISTICAL REQUIREMENT TO REPRESENT ALL OF CONFORMATIONAL SPACE CONSISTENT WITH THE DATA.
Conformers calculated total number: 50 / Conformers submitted total number: 24

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