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- PDB-5omp: Human FKBP5 protein -

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Basic information

Entry
Database: PDB / ID: 5omp
TitleHuman FKBP5 protein
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP51 / TPR / FK506 binding protein
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 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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 repeat 1 / Tetratricopeptide repeat / 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
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsKumar, R. / Moche, M. / Winblad, B. / Pavlov, P.
Funding support Sweden, 6items
OrganizationGrant numberCountry
Swedish Research Council2015-02774 Sweden
Stiftelsen For Gamla Tjanarinnor2016-00302 Sweden
Gun och Bertil Stohnes stiftelse4-2919/2016 Sweden
Gunvor och Josef Aners stiftelseFB16-0111 Sweden
Tore Nilsons stiftelse for medicinsk forskning2016-00304 Sweden
Foundation for Geriatric Diseases at Karolinska Institutet2016alde51194 Sweden
CitationJournal: Sci Rep / Year: 2017
Title: Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51.
Authors: Kumar, R. / Moche, M. / Winblad, B. / Pavlov, P.F.
History
DepositionAug 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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

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)51,9904
Polymers51,7021
Non-polymers2883
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-33 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.732, 90.732, 133.596
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 51701.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The full length human FKBP51 containing first 5 N-terminus amino acids from the expression vector.
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 3.07 Å3/Da / Density % sol: 59.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20 %w/v PEG MME 5K, 0.2 M NH4SO4, 0.1 M MES 6 pH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.88→133.593 Å / Num. all: 527164 / Num. obs: 27180 / % possible obs: 52.1 % / Redundancy: 19.4 % / Biso Wilson estimate: 42.69 Å2 / Net I/σ(I): 20.3
Reflection shellResolution: 1.88→2.15 Å / Redundancy: 17 % / Rmerge(I) obs: 1.556 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1347 / CC1/2: 0.763 / Rpim(I) all: 0.385 / Rsym value: 1.604 / % possible all: 8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSVERSION Jun 1, 2017 BUILT=20170601data reduction
STARANISOVersion 1.7.4 (19-Jun-17)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NJX

5njx


Resolution: 1.88→78.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.276 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1314 4.85 %RANDOM
Rwork0.198 ---
obs0.2 27108 51.8 %-
Displacement parametersBiso mean: 57.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.0071 Å20 Å20 Å2
2--1.0071 Å20 Å2
3----2.0142 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.88→78.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 15 348 3619
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013365HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.14509HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1248SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes482HARMONIC5
X-RAY DIFFRACTIONt_it3365HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion18.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion412SEMIHARMONIC5
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_contact3641SEMIHARMONIC4
LS refinement shellResolution: 1.88→1.95 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.4622 -1.49 %
Rwork0.2353 --
all0.2384 67 -
obs--1.24 %
Refinement TLS params.Method: refined / Origin x: 41.1342 Å / Origin y: -10.3327 Å / Origin z: -33.307 Å
111213212223313233
T0.0368 Å2-0.0093 Å2-0.0085 Å2--0.0023 Å2-0.0238 Å2---0.0237 Å2
L0.5073 °2-0.0909 °2-0.1884 °2-0.8765 °2-0.6461 °2--1.5948 °2
S-0.0662 Å °-0.0557 Å °-0.011 Å °0.0711 Å °0.0938 Å °0.0889 Å °-0.0226 Å °-0.1444 Å °-0.0276 Å °
Refinement TLS groupSelection details: { A|* }

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