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- PDB-6rcy: CRYSTAL STRUCTURE OF FK1 DOMAIN OF FKBP52 IN COMPLEX WITH A BIO-I... -

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Basic information

Entry
Database: PDB / ID: 6rcy
TitleCRYSTAL STRUCTURE OF FK1 DOMAIN OF FKBP52 IN COMPLEX WITH A BIO-INSPIRED HYBRID FLUORESCENT LIGAND
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP4
KeywordsISOMERASE / FKBP52 / THE N-TERMINAL DOMAIN / Ligand / Fluorescence
Function / homology
Function and homology information


steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / copper ion transport / nuclear glucocorticoid receptor binding / protein-containing complex localization / negative regulation of microtubule polymerization / FK506 binding ...steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / copper ion transport / nuclear glucocorticoid receptor binding / protein-containing complex localization / negative regulation of microtubule polymerization / FK506 binding / androgen receptor signaling pathway / Attenuation phase / axonal growth cone / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / embryo implantation / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / tau protein binding / protein folding / negative regulation of neuron projection development / protein-macromolecule adaptor activity / microtubule / Estrogen-dependent gene expression / Potential therapeutics for SARS / neuronal cell body / GTP binding / perinuclear region of cytoplasm / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat 2 / 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 ...Tetratricopeptide repeat 2 / 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-K0T / Peptidyl-prolyl cis-trans isomerase FKBP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi de la Sierra-Gallay, I. / Byrne, C.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Bioinspired Hybrid Fluorescent Ligands for the FK1 Domain of FKBP52.
Authors: de la Sierra-Gallay, I.L. / Belnou, M. / Chambraud, B. / Genet, M. / van Tilbeurgh, H. / Aumont-Nicaise, M. / Desmadril, M. / Baulieu, E.E. / Jacquot, Y. / Byrne, C.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9052
Polymers16,2251
Non-polymers6801
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7460 Å2
Unit cell
Length a, b, c (Å)52.960, 52.960, 237.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP4 / PPIase FKBP4 / 51 kDa FK506-binding protein / FKBP51 / 52 kDa FK506-binding protein / FKBP-52 / 59 ...PPIase FKBP4 / 51 kDa FK506-binding protein / FKBP51 / 52 kDa FK506-binding protein / FKBP-52 / 59 kDa immunophilin / p59 / FK506-binding protein 4 / FKBP-4 / FKBP59 / HSP-binding immunophilin / HBI / Immunophilin FKBP52 / Rotamase


Mass: 16225.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL FRAGMENT / Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP4, FKBP52 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02790, peptidylprolyl isomerase
#2: Chemical ChemComp-K0T / (2~{S})-5-carbamimidamido-2-[[(2~{S})-2-[[(2~{S})-1-[5-(dimethylamino)naphthalen-1-yl]sulfonylpiperidin-2-yl]carbonylamino]-4-phenyl-butanoyl]amino]pentanoic acid


Mass: 679.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H45N7O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8M potassium phosphate, 0.8M sodium phosphate, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→45.8 Å / Num. obs: 9583 / % possible obs: 99.6 % / Redundancy: 20.3 % / Biso Wilson estimate: 70.46 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.127 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.4 Å / Num. unique obs: 1440 / CC1/2: 0.78 / Rrim(I) all: 2.405

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N1A

1n1a


Resolution: 2.3→45.03 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.243 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.244 480 5.01 %RANDOM
Rwork0.218 ---
obs0.22 9581 99.6 %-
Displacement parametersBiso mean: 88.89 Å2
Baniso -1Baniso -2Baniso -3
1--8.1862 Å20 Å20 Å2
2---8.1862 Å20 Å2
3---16.3725 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.3→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1017 0 48 12 1077
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0091091HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.171475HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d388SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes203HARMONIC5
X-RAY DIFFRACTIONt_it1091HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion19.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion133SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1196SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.34 Å / Total num. of bins used: 24
RfactorNum. reflection% reflection
Rfree0.2799 -5 %
Rwork0.2527 380 -
all0.2539 400 -
obs--91.2 %
Refinement TLS params.Method: refined / Origin x: -18.5488 Å / Origin y: 19.855 Å / Origin z: -0.1813 Å
111213212223313233
T-0.4882 Å2-0.026 Å20.0392 Å2-0.341 Å2-0.0643 Å2---0.3285 Å2
L5.64 °2-0.2454 °22.0273 °2-2.4884 °21.0837 °2--4.6145 °2
S-0.0019 Å °-1.2705 Å °-0.0255 Å °0.1117 Å °0.0969 Å °0.0296 Å °0.2816 Å °-0.4521 Å °-0.095 Å °
Refinement TLS groupSelection details: { A|* }

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