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- PDB-2maz: Backbone 1H, 13C, and 15N Chemical Shift Assignments for Bovine A... -

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Basic information

Entry
Database: PDB / ID: 2maz
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for Bovine Apo Calbindin
ComponentsProtein S100-G
KeywordsMETAL BINDING PROTEIN / Bovine Apo Calbindin
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 / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsRaikwal, N. / Kumar, D.
CitationJournal: To be Published
Title: Prot3DNMR: A Simple and Swift NMR Strategy for Three-Dimensional Structure Determination of Proteins
Authors: Raikwal, N. / Kumar, D.
History
DepositionJul 22, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
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_spectrometer.model / _struct_ref_seq_dif.details
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

Downloads & links

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Assembly

Deposited unit
A: Protein S100-G


Theoretical massNumber of molelcules
Total (without water)8,5451
Polymers8,5451
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)20 / 20target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein S100-G / Calbindin-D9k / S100 calcium-binding protein G / Vitamin D-dependent calcium-binding protein / ...Calbindin-D9k / S100 calcium-binding protein G / Vitamin D-dependent calcium-binding protein / intestinal / CABP


Mass: 8544.637 Da / Num. of mol.: 1 / Fragment: UNP residues 5-79 / Mutation: P43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: S100G, CALB3, S100D / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / Variant (production host): BL21 / References: UniProt: P02633

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Prot3DNMR (An Efficient High-throughput NMR Method for Protein Fold Determination)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HNCA
NMR detailsText: The structure was determined using backbone amide NOEs and a few side chain NOEs obtained from 3D 13C HSQC-NOESY-15N-HSQC spectrum in combination with 3D-hCCcoNH spectrum.

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Sample preparation

DetailsContents: 1mM [U-100% 13C; U-100% 15N] D2O-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: D2O-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.02 / pH: 6.2 / Pressure: ambient / Temperature: 298 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
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 491 / NOE long range total count: 38 / NOE medium range total count: 374
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0 Å

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