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- PDB-4tw7: The Fk1 domain of FKBP51 in complex with iFit4 -

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Basic information

Entry
Database: PDB / ID: 4tw7
TitleThe Fk1 domain of FKBP51 in complex with iFit4
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophiline / peptidyl-prolyl isomerase / ligand selectivity
Function / homology
Function and homology information


FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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. ...Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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
Chem-37K / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsGaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Almeida, O.F.X. / Ruehter, G. ...Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Almeida, O.F.X. / Ruehter, G. / Uhr, M. / Schmidt, M.V. / Touma, C. / Bracher, A. / Hausch, F.
Citation
Journal: Nat.Chem.Biol. / Year: 2015
Title: Selective inhibitors of the FK506-binding protein 51 by induced fit.
Authors: Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Sippel, C. / Zannas, A.S. / Draenert, R. / Binder, E.B. / ...Authors: Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Sippel, C. / Zannas, A.S. / Draenert, R. / Binder, E.B. / Almeida, O.F. / Ruhter, G. / Uhr, M. / Schmidt, M.V. / Touma, C. / Bracher, A. / Hausch, F.
#1: Journal: Acta Cryst. Sect. D / Year: 2011
Title: Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90
Authors: Bracher, A. / Kozany, C. / Thost, A.-K. / Hausch, F.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8272
Polymers14,0261
Non-polymers8011
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.262, 60.934, 38.059
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 14026.077 Da / Num. of mol.: 1 / Mutation: A19T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Plasmid: pProEx-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus RIL / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-37K / (1R)-3-(3,4-dimethoxyphenyl)-1-{3-[2-(morpholin-4-yl)ethoxy]phenyl}propyl (2S)-1-[(2S)-2-[(1S)-cyclohex-2-en-1-yl]-2-(3,4,5-trimethoxyphenyl)acetyl]piperidine-2-carboxylate


Mass: 800.976 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H60N2O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.25→38.32 Å / Num. all: 29892 / Num. obs: 29892 / % possible obs: 92.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 8.392 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.027 / Rrim(I) all: 0.053 / Rsym value: 0.046 / Net I/av σ(I): 11.667 / Net I/σ(I): 15.8 / Num. measured all: 104481
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.25-1.322.50.4061.9721229350.2980.4062.363.7
1.32-1.43.10.332.31184438780.2160.333.489
1.4-1.493.60.2333.31464240890.1410.2335.498.3
1.49-1.613.60.1415.51374038340.0850.1418.798.9
1.61-1.773.60.0997.81267535350.060.09912.498.8
1.77-1.983.60.05812.91154732380.0360.05819.399.3
1.98-2.283.60.039181020528740.0240.03926.799.3
2.28-2.793.50.03320.4856924490.0210.0333199.2
2.79-3.953.40.02425.1658219280.0150.02438.798.9
3.95-38.326.60.02622.4746511320.0110.02655.798.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALA3.2.25data scaling
MOLREPphasing
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TW6

4tw6


Resolution: 1.25→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1723 / WRfactor Rwork: 0.1261 / FOM work R set: 0.9088 / SU B: 1.522 / SU ML: 0.03 / SU R Cruickshank DPI: 0.0465 / SU Rfree: 0.0485 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 1523 5.1 %RANDOM
Rwork0.1289 28336 --
obs0.1313 29859 92.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.82 Å2 / Biso mean: 13.462 Å2 / Biso min: 2.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0 Å2
2---0.34 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: final / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 58 215 1242
Biso mean--11.41 30.02 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021096
X-RAY DIFFRACTIONr_bond_other_d0.0020.021057
X-RAY DIFFRACTIONr_angle_refined_deg2.2092.0441482
X-RAY DIFFRACTIONr_angle_other_deg0.9213.0082383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3625137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16325.26338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46615188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.735152
X-RAY DIFFRACTIONr_chiral_restr0.1340.2155
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211220
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02213
X-RAY DIFFRACTIONr_rigid_bond_restr5.04632152
X-RAY DIFFRACTIONr_sphericity_free36.563542
X-RAY DIFFRACTIONr_sphericity_bonded11.6352296
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 70 -
Rwork0.215 1305 -
all-1375 -
obs--58.21 %

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