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- PDB-3o5d: Crystal structure of a fragment of FKBP51 comprising the Fk1 and ... -

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Basic information

Entry
Database: PDB / ID: 3o5d
TitleCrystal structure of a fragment of FKBP51 comprising the Fk1 and Fk2 domains
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophiline / peptidyl-prolyl isomerase
Function / homology
Function and homology information


FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / 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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. ...Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / 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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / 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: 4 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
B: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)58,4822
Polymers58,4822
Non-polymers00
Water0
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)29,2411
Polymers29,2411
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)29,2411
Polymers29,2411
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.730, 113.730, 112.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41

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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: 29241.076 Da / Num. of mol.: 2
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

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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: 60.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2M (NH4)3-citrate, 20% PEG3350, pH 7.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→80.42 Å / Num. all: 6065 / Num. obs: 6065 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.177 / Rsym value: 0.177 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
4-4.223.40.711.130168810.7199.8
4.22-4.473.40.5581.428808440.558100
4.47-4.783.40.3322.326367760.33299.9
4.78-5.163.40.32.525077420.399.6
5.16-5.663.40.2862.622136590.28699.7
5.66-6.323.30.2562.920386160.25699.7
6.32-7.33.20.184.117075350.1899.4
7.3-8.943.20.06910.314924680.06999.6
8.94-12.653.50.04513.912293530.04599.9
12.65-35.9673.20.04413.26051910.04494.3

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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 1Q1C

1q1c


Resolution: 4→20 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.807 / WRfactor Rfree: 0.3706 / WRfactor Rwork: 0.3555 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7054 / SU B: 225.421 / SU ML: 1.368 / SU R Cruickshank DPI: 1.2278 / SU Rfree: 1.2425 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3438 275 4.6 %RANDOM
Rwork0.3174 ---
obs0.3187 6023 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 319.76 Å2 / Biso mean: 164.8201 Å2 / Biso min: 81.03 Å2
Baniso -1Baniso -2Baniso -3
1-9.22 Å20 Å20 Å2
2--9.22 Å20 Å2
3----18.44 Å2
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 0 0 3742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223816
X-RAY DIFFRACTIONr_angle_refined_deg0.8151.9785120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6585482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.51224.353170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21315696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2611522
X-RAY DIFFRACTIONr_chiral_restr0.0560.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022886
X-RAY DIFFRACTIONr_nbd_refined0.1640.21530
X-RAY DIFFRACTIONr_nbtor_refined0.2960.22551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.26
X-RAY DIFFRACTIONr_mcbond_it0.0771.52465
X-RAY DIFFRACTIONr_mcangle_it0.1423800
X-RAY DIFFRACTIONr_scbond_it0.14331522
X-RAY DIFFRACTIONr_scangle_it0.2554.51320
LS refinement shellResolution: 4→4.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 18 -
Rwork0.396 419 -
all-437 -
obs--99.54 %
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)
18.12070.12734.6965.46174.098516.13760.13382.0809-1.1643-0.61740.11350.6640.9333-1.247-0.24730.1158-0.6161-0.187-0.80790.06610.8141-40.1384-10.11-5.5041
210.31013.87031.803813.42584.802118.6988-0.1332-0.3786-0.058-1.2113-0.28540.35670.59140.64030.4186-0.95810.1386-0.126-0.8776-0.0092-0.9884-22.563115.55655.6966
312.17252.505-5.4417.8198-2.09417.53680.1943-0.5109-0.77341.4222-0.21221.00351.2689-2.10880.0179-0.3456-0.4084-0.1121-0.37150.29540.7373-67.12916.759827.5144
421.02565.55173.659710.59621.612523.69550.4549-0.7671-0.1158-0.3063-0.33470.4651-1.0087-0.5167-0.1203-1.0180.17130.0379-0.95570.1289-0.9467-41.224134.113816.4383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 138
2X-RAY DIFFRACTION2A139 - 254
3X-RAY DIFFRACTION3B13 - 138
4X-RAY DIFFRACTION4B139 - 254

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