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- PDB-2d9f: Solution structure of RUH-047, an FKBP domain from human cDNA -

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Basic information

Entry
Database: PDB / ID: 2d9f
TitleSolution structure of RUH-047, an FKBP domain from human cDNA
ComponentsFK506-binding protein 8 variant
KeywordsISOMERASE / FKBP / FK506 binding protein / Rapamycin / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


neuron fate specification / regulation of mitophagy / dorsal/ventral neural tube patterning / protein localization to mitochondrion / positive regulation of BMP signaling pathway / mitochondrial envelope / camera-type eye development / smoothened signaling pathway / BMP signaling pathway / endomembrane system ...neuron fate specification / regulation of mitophagy / dorsal/ventral neural tube patterning / protein localization to mitochondrion / positive regulation of BMP signaling pathway / mitochondrial envelope / camera-type eye development / smoothened signaling pathway / BMP signaling pathway / endomembrane system / protein folding chaperone / negative regulation of protein phosphorylation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mitochondrial membrane / multicellular organism growth / disordered domain specific binding / protein folding / regulation of gene expression / calmodulin binding / intracellular signal transduction / Ub-specific processing proteases / endoplasmic reticulum membrane / negative regulation of apoptotic process / apoptotic process / endoplasmic reticulum / protein-containing complex / mitochondrion / identical protein binding / membrane / metal ion binding / cytosol
Similarity search - Function
: / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. ...: / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Peptidyl-prolyl cis-trans isomerase FKBP8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRuhul Momen, A.Z.M. / Hirota, H. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RUH-047, an FKBP domain from human cDNA
Authors: Ruhul Momen, A.Z.M. / Hirota, H. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionDec 9, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: 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 1.4May 29, 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: FK506-binding protein 8 variant


Theoretical massNumber of molelcules
Total (without water)14,2191
Polymers14,2191
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 / 100target function,structures with the lowest energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein FK506-binding protein 8 variant / FK506-Binding Domain / FKBP


Mass: 14219.016 Da / Num. of mol.: 1 / Fragment: Residues 8-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P040614-07 / References: GenBank: 62897235, UniProt: Q14318*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.01mM domain U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM NaCl / pH: 7 / 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
XwinNMR3.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.04Johnson, B.A.data analysis
KUJIRA0.9295Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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