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- PDB-2f2d: Solution structure of the FK506-binding domain of human FKBP38 -

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Basic information

Entry
Database: PDB / ID: 2f2d
TitleSolution structure of the FK506-binding domain of human FKBP38
Components38 kDa FK-506 binding protein homolog, FKBP38
KeywordsISOMERASE / beta half-barrel / PPIase / immunophilin
Function / homology
Function and homology information


neuron fate specification / regulation of autophagy of mitochondrion / dorsal/ventral neural tube patterning / protein localization to mitochondrion / positive regulation of BMP signaling pathway / mitochondrial envelope / camera-type eye development / smoothened signaling pathway / endomembrane system / BMP signaling pathway ...neuron fate specification / regulation of autophagy of mitochondrion / dorsal/ventral neural tube patterning / protein localization to mitochondrion / positive regulation of BMP signaling pathway / mitochondrial envelope / camera-type eye development / smoothened signaling pathway / endomembrane system / BMP signaling pathway / 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 / Ub-specific processing proteases / intracellular signal transduction / apoptotic process / endoplasmic reticulum membrane / negative regulation of apoptotic process / endoplasmic reticulum / protein-containing complex / mitochondrion / membrane / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Tetratricopeptide repeat 2 / 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 2 / 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 / simulated annealing, torsion angle dynamics, energy minimization
AuthorsMaestre-Martinez, M. / Edlich, F. / Jarczowski, F. / Weiwad, M. / Fischer, G. / Luecke, C.
CitationJournal: J.BIOMOL.NMR / Year: 2006
Title: Solution Structure of the FK506-Binding Domain of Human FKBP38
Authors: Maestre-Martinez, M. / Edlich, F. / Jarczowski, F. / Weiwad, M. / Fischer, G. / Luecke, C.
History
DepositionNov 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 38 kDa FK-506 binding protein homolog, FKBP38


Theoretical massNumber of molelcules
Total (without water)13,0681
Polymers13,0681
Non-polymers00
Water0
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
RepresentativeModel #1fewest violations

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Components

#1: Protein 38 kDa FK-506 binding protein homolog, FKBP38 / FKBPR38 / FK506-binding protein 8


Mass: 13067.957 Da / Num. of mol.: 1 / Fragment: FK506-binding domain, residues 35-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP8, FKBP38 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14318

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1322D 15N-separated HSQC
1422D 15N-separated HTQC
1523D 15N-separated TOCSY
1623D 15N-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.3 mM hFKBP38D, 20 mM phosphate buffer, 0.05% azide, 95% H2O, 5% D2O95% H2O/5% D2O
21.3 mM hFKBP38D U-15N, 20 mM phosphate buffer, 0.05% azide, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukerprocessing
AURELIA2.5.9Brukerdata analysis
Felix2000Accelrysdata analysis
DYANA1.5Guentertstructure solution
Discover2000Accelrysrefinement
RefinementMethod: simulated annealing, torsion angle dynamics, energy minimization
Software ordinal: 1
Details: the structures are based on 1585 NOE-derived distants restraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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