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- PDB-1t6w: RATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STR... -

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Entry
Database: PDB / ID: 1t6w
TitleRATIONAL DESIGN OF A CALCIUM-BINDING ADHESION PROTEIN NMR, 20 STRUCTURES
Componentshypothetical protein XP_346638
KeywordsMETAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN / CD2 / DESIGN
Function / homology
Function and homology information


natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / positive regulation of interleukin-8 production / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / cell-cell adhesion / : / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production ...natural killer cell mediated cytotoxicity / natural killer cell activation / heterotypic cell-cell adhesion / positive regulation of interleukin-8 production / cytoplasmic side of plasma membrane / receptor tyrosine kinase binding / cell-cell adhesion / : / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell-cell junction / external side of plasma membrane / signaling receptor binding / protein kinase binding / Golgi apparatus / cell surface / protein-containing complex / extracellular region / nucleoplasm / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface antigen CD2 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface antigen CD2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / ANNEAL
AuthorsYang, W. / Wilkins, A.L. / Ye, Y. / Liu, Z.-R. / Urbauer, J.L. / Kearney, A. / van der Merwe, P.A. / Yang, J.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2005
Title: Design of a calcium-binding protein with desired structure in a cell adhesion molecule.
Authors: Yang, W. / Wilkins, A.L. / Ye, Y. / Liu, Z.R. / Li, S.Y. / Urbauer, J.L. / Hellinga, H.W. / Kearney, A. / van der Merwe, P.A. / Yang, J.J.
History
DepositionMay 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: hypothetical protein XP_346638
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2002
Polymers11,1601
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein hypothetical protein XP_346638


Mass: 11159.620 Da / Num. of mol.: 1 / Mutation: N15D, N17D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PGEX-2T / Cell line (production host): BL21(DE3) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P08921
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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 NOESY
1212D TOCSY
1313D 15N-separated NOESY
1413D 15N-separated TOCSY
15115N-HSQC

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Sample preparation

DetailsContents: 95% H2O, 5% D2O, protein 1 mM, KCl 130 mM, CaCl2 10 mM, PIPES 20 mM
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGERrefinement
CNS1.1BRUNGERstructure solution
RefinementMethod: ANNEAL / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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