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- PDB-3o5k: Fk1 domain of FKBP51, crystal form VIII -

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Basic information

Entry
Database: PDB / ID: 3o5k
TitleFk1 domain of FKBP51, crystal form VIII
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: 2.7 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

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
B: Peptidyl-prolyl cis-trans isomerase FKBP5
C: Peptidyl-prolyl cis-trans isomerase FKBP5
D: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)55,9844
Polymers55,9844
Non-polymers00
Water00
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)13,9961
Polymers13,9961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)13,9961
Polymers13,9961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)13,9961
Polymers13,9961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)13,9961
Polymers13,9961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.802, 48.430, 76.317
Angle α, β, γ (deg.)90.000, 114.500, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4
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

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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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 32 % PEG3350, 0.05 M NH4OAc, 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: 2.7→69.505 Å / Num. all: 12932 / Num. obs: 12932 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 53.37 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.853.60.3921.9677618900.39299.7
2.85-3.023.60.282.7635517770.2899.7
3.02-3.233.60.1824.1591816570.18299.2
3.23-3.493.50.135.6544915660.1399.5
3.49-3.823.40.0878.3483114100.08798.9
3.82-4.273.20.05911.2398912590.05997.2
4.27-4.933.70.04612.1424711590.04699.9
4.93-6.043.70.078.536589900.07100
6.04-8.543.60.04314.128117720.043100
8.54-69.5053.40.02722.415424520.02799.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å69.45 Å
Translation3 Å69.45 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 3O5I, chain A

3o5i


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.868 / WRfactor Rfree: 0.2825 / WRfactor Rwork: 0.2469 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7951 / SU B: 35.643 / SU ML: 0.329 / SU R Cruickshank DPI: 0.3783 / SU Rfree: 0.4413 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 629 4.9 %RANDOM
Rwork0.2239 ---
obs0.2267 12890 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.14 Å2 / Biso mean: 47.7977 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.82 Å2
2---1.44 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3794 0 0 0 3794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223874
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9725223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65624.468141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11115655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8991511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022887
X-RAY DIFFRACTIONr_nbd_refined0.2080.21589
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22592
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.26
X-RAY DIFFRACTIONr_mcbond_it0.3531.52568
X-RAY DIFFRACTIONr_mcangle_it0.63223989
X-RAY DIFFRACTIONr_scbond_it0.87431466
X-RAY DIFFRACTIONr_scangle_it1.4034.51234
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 46 -
Rwork0.292 872 -
all-918 -
obs--99.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5158-1.123-1.53536.4419-0.19984.896-0.0371-0.15570.02530.31830.008-0.0228-0.1158-0.04040.0291-0.2353-0.0157-0.0291-0.1730.0279-0.22610.35580.53115.7032
28.9289-1.6076-1.60376.35390.15332.75480.0569-0.25260.41540.19550.1346-0.2532-0.11450.0709-0.1915-0.1923-0.0333-0.0253-0.1674-0.0227-0.107431.20131.12564.6837
36.4196-1.6386-2.89510.213-0.97137.54050.1733-0.42810.34850.5633-0.1869-0.4056-0.65660.44730.01370.0336-0.12350.0421-0.06220.0067-0.15617.4581-2.0425-29.1122
410.9262.70823.71358.98580.63135.65450.09140.9356-1.1258-0.93390.4225-1.62930.11190.4085-0.51390.27760.0550.10020.2098-0.00510.51617.0764-17.112929.6999
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 139
2X-RAY DIFFRACTION2B13 - 139
3X-RAY DIFFRACTION3C13 - 140
4X-RAY DIFFRACTION4D13 - 140

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