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- PDB-2kd2: NMR Structure of FAIM-CTD -

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Basic information

Entry
Database: PDB / ID: 2kd2
TitleNMR Structure of FAIM-CTD
ComponentsFas apoptotic inhibitory molecule 1
KeywordsAPOPTOSIS / PROTEIN / BETA SANDWICH
Function / homology
Function and homology information


positive regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of canonical NF-kappaB signal transduction / apoptotic process / cytoplasm
Similarity search - Function
Lipocalin - #180 / Fas apoptotic inhibitory molecule 1 / FAIM1 domain superfamily / Fas apoptotic inhibitory molecule (FAIM1) / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fas apoptotic inhibitory molecule 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsHemond, M. / Wagner, G.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Fas apoptosis inhibitory molecule contains a novel beta-sandwich in contact with a partially ordered domain.
Authors: Hemond, M. / Rothstein, T.L. / Wagner, G.
History
DepositionJan 1, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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: Fas apoptotic inhibitory molecule 1


Theoretical massNumber of molelcules
Total (without water)10,5211
Polymers10,5211
Non-polymers00
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Fas apoptotic inhibitory molecule 1


Mass: 10520.711 Da / Num. of mol.: 1 / Fragment: UNP residues 91-179 / Mutation: G63D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Faim, Faim1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WUD8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCO
1323D HNCO
1413D HN(CA)CO
1513D HNCA
1613D HN(CO)CA
1713D HN(CA)CB
1813D CBCA(CO)NH
1913D HNCO
11053D 1H-15N NOESY
11153D 1H-15N TOCSY
11213D C(CO)NH
11313D H(CCO)NH
11432D 1H-13C HSQC
11533D 1H-13C NOESY
11662D 1H-1H NOESY
11713D (H)CCH-TOCSY
11832D CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.25-0.5 mM [U-99% 13C; U-99% 15N] FAIM-CTD, 10 mM sodium chloride, 10 mM TRIS, 5 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
20.25 mM [U-99% 13C; U-99% 15N] FAIM-CTD, 10 mM sodium chloride, 10 mM TRIS, 5 mM DTT, 0.6% w/v Pf1 filamentous phage, 95% H2O/5% D2O95% H2O/5% D2O
31.8 mM [U-99% 13C] FAIM-CTD, 10 mM sodium chloride, 10 mM TRIS, 5 mM DTT, 100% D2O100% D2O
40.5 mM [U-10% 13C] FAIM-CTD, 10 mM sodium chloride, 10 mM TRIS, 5 mM DTT, 100% D2O100% D2O
50.25-0.9 mM [U-99% 15N] FAIM-CTD, 10 mM sodium chloride, 10 mM TRIS, 5 mM DTT, 95% H2O/5% D2O95% H2O/5% D2O
61.0 mM FAIM-CTD, 10 mM sodium chloride, 10 mM TRIS, 5 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMFAIM-CTD-1[U-99% 13C; U-99% 15N]0.25-0.51
10 mMsodium chloride-21
10 mMTRIS-31
5 mMDTT-41
0.25 mMFAIM-CTD-5[U-99% 13C; U-99% 15N]2
10 mMsodium chloride-62
10 mMTRIS-72
5 mMDTT-82
0.6 %Pf1 filamentous phage-92
1.8 mMFAIM-CTD-10[U-99% 13C]3
10 mMsodium chloride-113
10 mMTRIS-123
5 mMDTT-133
0.5 mMFAIM-CTD-14[U-10% 13C]4
10 mMsodium chloride-154
10 mMTRIS-164
5 mMDTT-174
mMFAIM-CTD-18[U-99% 15N]0.25-0.95
10 mMsodium chloride-195
10 mMTRIS-205
5 mMDTT-215
1.0 mMFAIM-CTD-226
10 mMsodium chloride-236
10 mMTRIS-246
5 mMDTT-256
Sample conditionsIonic strength: 10 / pH: 7.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4 Rev 2006.095.11.35Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.11Goddarddata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1008 / NOE intraresidue total count: 193 / NOE long range total count: 421 / NOE medium range total count: 114 / NOE sequential total count: 206 / Hydrogen bond constraints total count: 32 / Protein chi angle constraints total count: 21 / Protein other angle constraints total count: 16 / Protein phi angle constraints total count: 53 / Protein psi angle constraints total count: 53
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.37 Å

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