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- PDB-3o5f: Fk1 domain of FKBP51, crystal form VII -

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Basic information

Entry
Database: PDB / ID: 3o5f
TitleFk1 domain of FKBP51, crystal form VII
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 / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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 / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / 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
CARBONATE ION / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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)15,7682
Polymers15,7081
Non-polymers601
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.679, 49.703, 66.978
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: 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: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.89 Å3/Da / Density % sol: 34.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 30 % PEG2000MME, 0.1 M KSCN, pH 8.0, 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: 1.65→39.914 Å / Num. all: 14796 / Num. obs: 14796 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 23.31 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.743.40.4551.7716120920.45598.6
1.74-1.843.50.2712.8687519850.27198.7
1.84-1.973.50.1644.2670019090.16499.7
1.97-2.133.50.1135.9623017590.11399.5
2.13-2.333.50.0866.7581616410.08699.7
2.33-2.613.50.069.5530115030.0699.9
2.61-3.013.50.04512.8468413330.04599.9
3.01-3.693.50.04611.5394511350.04699.9
3.69-5.223.40.0317.531219190.0399.8
5.22-39.9043.10.0183416265200.01896.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.461 / Cor.coef. Fo:Fc: 0.533
Highest resolutionLowest resolution
Rotation2.5 Å28.98 Å
Translation2.5 Å28.98 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: 1.65→19.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.236 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8531 / SU B: 5.029 / SU ML: 0.085 / SU R Cruickshank DPI: 0.1277 / SU Rfree: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 748 5.1 %RANDOM
Rwork0.197 ---
obs0.1989 14752 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.29 Å2 / Biso mean: 32.1871 Å2 / Biso min: 13.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 4 90 1051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221052
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9731422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89524.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72115197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.588154
X-RAY DIFFRACTIONr_chiral_restr0.1020.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02798
X-RAY DIFFRACTIONr_nbd_refined0.2040.2476
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2738
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.25
X-RAY DIFFRACTIONr_mcbond_it0.7981.5686
X-RAY DIFFRACTIONr_mcangle_it1.19321072
X-RAY DIFFRACTIONr_scbond_it2.2163412
X-RAY DIFFRACTIONr_scangle_it3.0364.5350
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 61 -
Rwork0.27 992 -
all-1053 -
obs--98.6 %
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)
112.429817.02953.1724.84949.390317.58940.1750.9391-0.1774-0.67171.02660.7520.64191.1607-1.20160.51270.0123-0.21750.2696-0.07490.144118.609924.32320.4157
24.3897-2.818-0.52359.30060.41410.9227-0.07380.00950.07190.2432-0.0762-0.00220.04510.08180.1499-0.204-0.00930.0151-0.15230.0454-0.228323.332328.930614.6895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 21
2X-RAY DIFFRACTION2A22 - 139

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