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- PDB-3o5e: Fk1 domain of FKBP51, crystal form VI -

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Basic information

Entry
Database: PDB / ID: 3o5e
TitleFk1 domain of FKBP51, crystal form VI
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophiline / peptidyl-prolyl isomerase
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 / peptidylprolyl isomerase ...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 / peptidylprolyl isomerase / response to bacterium / 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
Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsBracher, A. / Kozany, C. / Thost, A.-K. / Hausch, F.
CitationJournal: Acta Crystallogr.,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
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,7081
Polymers15,7081
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.381, 54.381, 90.155
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

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Components

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


Mass: 15707.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIG6, FKBP5, FKBP51 / Plasmid: pProEx-HtA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.8 M (NH4)3citrate, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.972 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.6→47.096 Å / Num. all: 20975 / Num. obs: 20975 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.19 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.694.40.4091.81302129930.409100
1.69-1.794.40.2592.81257828680.259100
1.79-1.914.40.1813.91178626850.181100
1.91-2.074.40.13951108925210.139100
2.07-2.264.40.1185.71016223150.118100
2.26-2.534.40.1086922320890.10899.9
2.53-2.924.40.0966.7831318930.09699.9
2.92-3.584.30.0787.9690515930.078100
3.58-5.064.20.0659.4537912710.06599.9
5.06-41.7433.90.05411.129367470.05498.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.601 / Cor.coef. Fo:Fc: 0.305
Highest resolutionLowest resolution
Rotation3 Å35.97 Å
Translation3 Å35.97 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O5P

3o5p


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2407 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8693 / SU B: 3.578 / SU ML: 0.058 / SU R Cruickshank DPI: 0.1076 / SU Rfree: 0.0904 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1076 5.1 %RANDOM
Rwork0.1873 ---
obs0.1893 20926 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.74 Å2 / Biso mean: 21.2515 Å2 / Biso min: 4.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 0 108 1081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221077
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9751460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1615144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62524.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85215199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.016154
X-RAY DIFFRACTIONr_chiral_restr0.1230.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02820
X-RAY DIFFRACTIONr_nbd_refined0.2270.2473
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2754
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.212
X-RAY DIFFRACTIONr_mcbond_it1.211.5708
X-RAY DIFFRACTIONr_mcangle_it1.7321109
X-RAY DIFFRACTIONr_scbond_it3.0123421
X-RAY DIFFRACTIONr_scangle_it3.7994.5351
X-RAY DIFFRACTIONr_rigid_bond_restr2.48531129
X-RAY DIFFRACTIONr_sphericity_free4.5593117
X-RAY DIFFRACTIONr_sphericity_bonded3.35431048
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 88 -
Rwork0.225 1413 -
all-1501 -
obs--100 %

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