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- PDB-1kt1: Structure of the Large FKBP-like Protein, FKBP51, Involved in Ste... -

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Basic information

Entry
Database: PDB / ID: 1kt1
TitleStructure of the Large FKBP-like Protein, FKBP51, Involved in Steroid Receptor Complexes
ComponentsFK506-binding protein FKBP51
KeywordsISOMERASE / FKBP-like PPIase / TPR repeats
Function / homology
Function and homology information


FK506 binding / chaperone-mediated protein folding / heat shock protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / nucleoplasm / cytoplasm
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase FKBP5 / : / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain ...Peptidyl-prolyl cis-trans isomerase FKBP5 / : / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesSaimiri boliviensis (Bolivian squirrel monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSinars, C.R. / Cheung-Flynn, J. / Rimerman, R.A. / Scammell, J.G. / Smith, D.F. / Clardy, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: STRUCTURE OF THE LARGE FK506-BINDING PROTEIN FKBP51, AN HSP90-BINDING PROTEIN AND A COMPONENT OF STEROID RECEPTOR COMPLEXES
Authors: Sinars, C.R. / Cheung-Flynn, J. / Rimerman, R.A. / Scammell, J.G. / Smith, D.F. / Clardy, J.C.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FK506-binding protein FKBP51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4433
Polymers51,2511
Non-polymers1922
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.035, 91.035, 132.648
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 FK506-binding protein FKBP51


Mass: 51251.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saimiri boliviensis (Bolivian squirrel monkey)
Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9XSH5, peptidylprolyl isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.1 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: PEGMME 5000, ammonium sulfate, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
350 mM1dropNaCl
40.1 mMEDTA1drop
510 mMdithiothreitol1drop
615-18 %PEG5000 MME1reservoir
7100 mMMES1reservoirpH5.8
80.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9251 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9251 Å / Relative weight: 1
ReflectionResolution: 2.8→45 Å / Num. all: 16210 / Num. obs: 16210 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.9 % / Biso Wilson estimate: 45.4 Å2 / Rsym value: 0.087 / Net I/σ(I): 6.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2333 / Rsym value: 0.421 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 45 Å / Num. obs: 16161 / % possible obs: 100 % / Num. measured all: 95940 / Rmerge(I) obs: 0.087

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→43.05 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1287156.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 812 5 %RANDOM
Rwork0.255 ---
all-16210 --
obs-16179 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.489 Å2 / ksol: 0.361961 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1-13.07 Å211.28 Å20 Å2
2--13.07 Å20 Å2
3----26.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 10 31 3012
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it3.62.5
X-RAY DIFFRACTIONc_mcangle_it5.524
X-RAY DIFFRACTIONc_scbond_it6.394
X-RAY DIFFRACTIONc_scangle_it8.354.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 136 5.1 %
Rwork0.339 2525 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 45 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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