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- PDB-3o5g: Fk1 domain of FKBP51, crystal form I -

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Basic information

Entry
Database: PDB / ID: 3o5g
TitleFk1 domain of FKBP51, crystal form I
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: 2 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)13,9961
Polymers13,9961
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.993, 46.993, 89.767
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 13996.051 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-HtB / 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.: 63 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 35% PEG3350, 0.1 M HEPES, pH 7.5, 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: 2→40.697 Å / Num. all: 8222 / Num. obs: 8222 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 30.44 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 17.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.116.90.6671.1808411750.667100
2.11-2.246.90.4611.6773811200.461100
2.24-2.396.80.2872.6705910360.28799.9
2.39-2.586.80.1933.866349790.193100
2.58-2.836.80.1395.261339070.139100
2.83-3.166.60.0817.955228310.081100
3.16-3.656.50.05610.947817370.05699.8
3.65-4.476.20.0629.539206300.06299.8
4.47-6.325.90.0677.729214980.06799.4
6.32-89.8035.70.0316.917653090.0398.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å37.06 Å
Translation2.5 Å37.06 Å

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Processing

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

3o5p


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.1965 / WRfactor Rwork: 0.1675 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9135 / SU B: 9.042 / SU ML: 0.133 / SU R Cruickshank DPI: 0.0372 / SU Rfree: 0.0375 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 376 4.6 %RANDOM
Rwork0.1908 ---
obs0.1942 8185 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.51 Å2 / Biso mean: 34.3775 Å2 / Biso min: 18.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.37 Å20 Å2
2--0.75 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 63 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022996
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9771339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.7995127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05124.87239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43615180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.575153
X-RAY DIFFRACTIONr_chiral_restr0.1190.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02741
X-RAY DIFFRACTIONr_nbd_refined0.20.2428
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.213
X-RAY DIFFRACTIONr_mcbond_it0.5761.5653
X-RAY DIFFRACTIONr_mcangle_it0.95521008
X-RAY DIFFRACTIONr_scbond_it1.6323394
X-RAY DIFFRACTIONr_scangle_it2.3414.5331
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 24 -
Rwork0.222 582 -
all-606 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 7.7999 Å / Origin y: -16.1424 Å / Origin z: 3.2321 Å
111213212223313233
T-0.0729 Å2-0.0294 Å2-0.0425 Å2--0.1544 Å20.0025 Å2---0.1229 Å2
L2.9814 °20.5217 °2-1.2825 °2-2.738 °2-0.7703 °2--4.0309 °2
S0.0178 Å °0.0001 Å °-0.0093 Å °0.0917 Å °-0.0414 Å °0.1208 Å °-0.2024 Å °-0.1723 Å °0.0236 Å °

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