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- PDB-3o5q: Fk1 domain mutant A19T of FKBP51, crystal form IV, in presence of DMSO -

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Basic information

Entry
Database: PDB / ID: 3o5q
TitleFk1 domain mutant A19T of FKBP51, crystal form IV, in presence of DMSO
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 / 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 / cytosol / cytoplasm
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 / Resolution: 0.96 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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)14,1823
Polymers14,0261
Non-polymers1562
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.396, 53.514, 56.381
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 14026.077 Da / Num. of mol.: 1 / Mutation: A19T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIG6, FKBP5, FKBP51 / Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT A19T IS A MUTATION, BUT NOT A NATURALLY OCCURRING ALLELE.

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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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 37.5 % PEG3350, 0.1 M NH4OAc, 0.1 M HEPES, 10 % DMSO, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.886 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 0.949→33.885 Å / Num. all: 74281 / Num. obs: 74281 / % possible obs: 94.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 5.19 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 19.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
0.949-1.012.90.32.62859499580.388.3
1.01-1.073.10.1744.43055798130.17491.6
1.07-1.153.30.116.93162794700.1193.5
1.15-1.243.50.08493141490170.08495.5
1.24-1.363.60.06611.32992683760.06696.2
1.36-1.523.60.05313.72754977000.05397.2
1.52-1.753.50.03818.42426768590.03898
1.75-2.153.50.02525.12018258020.02597.4
2.15-3.0450.02327.72331446430.02399
3.04-38.8145.40.01934.11438226430.01998.1

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O5P

3o5p


Resolution: 0.96→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1524 / WRfactor Rwork: 0.1312 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.945 / SU B: 0.439 / SU ML: 0.011 / SU R Cruickshank DPI: 0.0199 / SU Rfree: 0.0213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1525 3687 5 %RANDOM
Rwork0.1296 ---
obs0.1308 74221 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 40.68 Å2 / Biso mean: 9.7308 Å2 / Biso min: 3.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 0.96→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 8 242 1221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221153
X-RAY DIFFRACTIONr_bond_other_d0.0020.02803
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9821569
X-RAY DIFFRACTIONr_angle_other_deg0.88831977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6715158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.92824.31844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27715209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.626155
X-RAY DIFFRACTIONr_chiral_restr0.1010.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021348
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02232
X-RAY DIFFRACTIONr_nbd_refined0.2520.2239
X-RAY DIFFRACTIONr_nbd_other0.2190.2888
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2589
X-RAY DIFFRACTIONr_nbtor_other0.0870.2584
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.245
X-RAY DIFFRACTIONr_mcbond_it1.5941.5785
X-RAY DIFFRACTIONr_mcbond_other0.6061.5299
X-RAY DIFFRACTIONr_mcangle_it2.08721194
X-RAY DIFFRACTIONr_scbond_it2.9943466
X-RAY DIFFRACTIONr_scangle_it3.6934.5375
X-RAY DIFFRACTIONr_rigid_bond_restr1.21932189
X-RAY DIFFRACTIONr_sphericity_free6.4973260
X-RAY DIFFRACTIONr_sphericity_bonded3.52231924
LS refinement shellResolution: 0.96→0.985 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 247 -
Rwork0.188 4712 -
all-4959 -
obs--86.36 %

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