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- PDB-4w9o: The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-[(3,5-dich... -

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Basic information

Entry
Database: PDB / ID: 4w9o
TitleThe Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-5-[(1R)-1,2-dihydroxyethyl]-3-[2-(3,4-dimethoxyphenoxy)ethyl]-3,10-diazabicyclo[4.3.1]decan-2-one
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


Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / response to bacterium ...Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / response to bacterium / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily ...: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-3JQ / ACETATE ION / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.27 Å
AuthorsPomplun, S. / Wang, Y. / Kirschner, K. / Kozany, C. / Bracher, A. / Hausch, F.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Rational Design and Asymmetric Synthesis of Potent and Neurotrophic Ligands for FK506-Binding Proteins (FKBPs).
Authors: Pomplun, S. / Wang, Y. / Kirschner, A. / Kozany, 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
DepositionAug 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
E: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3776
Polymers28,0522
Non-polymers1,3254
Water5,405300
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6302
Polymers14,0261
Non-polymers6041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7484
Polymers14,0261
Non-polymers7223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.704, 50.586, 68.953
Angle α, β, γ (deg.)90.000, 115.540, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a monomer

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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.: 2 / Fragment: Fk1 domain, UNP residues 16-140 / Mutation: yes
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) / Strain (production host): codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-3JQ / (1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-5-[(1R)-1,2-dihydroxyethyl]-3-[2-(3,4-dimethoxyphenoxy)ethyl]-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 603.512 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H32Cl2N2O8S
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 39.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 34 % 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: ID29 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.27→40.06 Å / Num. obs: 59102 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.036 / Net I/σ(I): 10.5 / Num. measured all: 219497
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.27-1.293.60.6361.91002328150.6360.38596.1
6.96-40.063.80.03236.514853880.9980.01899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å40.06 Å
Translation3 Å40.06 Å

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
MOLREP10.2.35phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O5Q

3o5q


Resolution: 1.27→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1773 / WRfactor Rwork: 0.1412 / FOM work R set: 0.8941 / SU B: 1.691 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0479 / SU Rfree: 0.0477 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / 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
Rfree0.1775 2979 5 %RANDOM
Rwork0.1393 56123 --
obs0.1413 56123 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.08 Å2 / Biso mean: 14.999 Å2 / Biso min: 7.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å2-0 Å2-0.24 Å2
2---0.59 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 1.27→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 86 305 2318
Biso mean--11.32 25.71 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022169
X-RAY DIFFRACTIONr_bond_other_d0.0030.022097
X-RAY DIFFRACTIONr_angle_refined_deg1.5262.0162932
X-RAY DIFFRACTIONr_angle_other_deg0.8913.0094888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22524.69181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47615397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.26157
X-RAY DIFFRACTIONr_chiral_restr0.1240.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212420
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02457
X-RAY DIFFRACTIONr_rigid_bond_restr3.17934265
X-RAY DIFFRACTIONr_sphericity_free20.626562
X-RAY DIFFRACTIONr_sphericity_bonded6.21254453
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 226 -
Rwork0.233 4071 -
all-4297 -
obs--97.09 %

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