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- PDB-7r0l: Structure of the FK1 domain of the FKBP51 G64S variant in complex... -

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Basic information

Entry
Database: PDB / ID: 7r0l
TitleStructure of the FK1 domain of the FKBP51 G64S variant in complex with SAFit1
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Isomerase Inhibitor Complex
Function / homology
Function and homology information


FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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 / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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 / cytosol / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat / Tetratricopeptide repeat / 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 repeat / 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
Similarity search - Domain/homology
Chem-GY1 / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMeyners, C. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
Hessian Ministry of Science, Higher Education and Art (HMWK) Germany
CitationJournal: Front Mol Biosci / Year: 2022
Title: Binding pocket stabilization by high-throughput screening of yeast display libraries.
Authors: Lerma Romero, J.A. / Meyners, C. / Christmann, A. / Reinbold, L.M. / Charalampidou, A. / Hausch, F. / Kolmar, H.
History
DepositionFeb 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2045
Polymers14,0341
Non-polymers1,1704
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint7 kcal/mol
Surface area6710 Å2
Unit cell
Length a, b, c (Å)45.106, 48.592, 57.191
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 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor- ...PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 14034.053 Da / Num. of mol.: 1 / Mutation: A19T G64S C103A C107I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-GY1 / 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid


Mass: 747.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H53NO11 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG3350, 0.2 M NH4-acetate and HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→45.11 Å / Num. obs: 51727 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.039 / Rrim(I) all: 0.073 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.02-45.115.90.0233850.9990.0140.027
1.1-1.126.11.31625130.6830.8691.584

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TW6

4tw6


Resolution: 1.1→37.003 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.16 / WRfactor Rwork: 0.136 / SU B: 1.297 / SU ML: 0.026 / Average fsc free: 0.9188 / Average fsc work: 0.9263 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1706 2517 4.872 %
Rwork0.1431 49145 -
all0.144 --
obs-51662 99.861 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å2-0 Å2
2---0.874 Å20 Å2
3---0.114 Å2
Refinement stepCycle: LAST / Resolution: 1.1→37.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 81 145 1187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0131099
X-RAY DIFFRACTIONr_bond_other_d0.0050.0161038
X-RAY DIFFRACTIONr_angle_refined_deg2.1491.7151484
X-RAY DIFFRACTIONr_angle_other_deg1.7921.6722408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4235134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.00923.65941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.05515171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.503153
X-RAY DIFFRACTIONr_chiral_restr0.1170.2137
X-RAY DIFFRACTIONr_chiral_restr_other1.3810.217
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
X-RAY DIFFRACTIONr_nbd_refined0.2530.2211
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.2990
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2532
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.290
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1230.211
X-RAY DIFFRACTIONr_nbd_other0.1640.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.220
X-RAY DIFFRACTIONr_mcbond_it2.2661.389533
X-RAY DIFFRACTIONr_mcbond_other2.2681.389532
X-RAY DIFFRACTIONr_mcangle_it2.4012.092668
X-RAY DIFFRACTIONr_mcangle_other2.42.091669
X-RAY DIFFRACTIONr_scbond_it6.6731.632566
X-RAY DIFFRACTIONr_scbond_other6.6671.632567
X-RAY DIFFRACTIONr_scangle_it4.6432.346816
X-RAY DIFFRACTIONr_scangle_other4.642.346817
X-RAY DIFFRACTIONr_lrange_it5.43818.8871241
X-RAY DIFFRACTIONr_lrange_other5.09118.2831217
X-RAY DIFFRACTIONr_rigid_bond_restr10.51232137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.1-1.1290.2941900.27935920.2838030.780.77899.44780.276
1.129-1.1590.2461950.2534610.2536630.8150.82999.80890.239
1.159-1.1930.291640.2334020.23235680.8050.84799.94390.215
1.193-1.230.221520.20833070.20934640.8840.88999.85570.188
1.23-1.270.2091610.18432170.18533790.9140.91899.97040.165
1.27-1.3150.2071680.17330980.17532720.9210.92599.81660.151
1.315-1.3640.1811490.15830260.15931780.9420.94399.90560.137
1.364-1.420.1891400.14228640.14430050.950.95399.96670.12
1.42-1.4830.1771310.12628170.12829490.9540.9699.96610.106
1.483-1.5550.141430.10726600.10928060.9720.97499.89310.091
1.555-1.6390.151320.09325110.09626450.9720.98199.92440.08
1.639-1.7380.1591160.09824390.125580.9710.9899.88270.085
1.738-1.8580.1371420.09122220.09323640.9780.9851000.082
1.858-2.0060.1361280.09821010.122300.9770.98499.95520.091
2.006-2.1970.139880.10719740.10820660.980.98499.80640.103
2.197-2.4550.137990.11417670.11618720.9760.98199.67950.112
2.455-2.8330.165780.13615950.13716740.9690.97399.94030.138
2.833-3.4650.183610.14613730.14814340.970.9731000.154
3.465-4.8790.164490.14310770.14411290.9720.97899.73430.165
4.879-37.0030.174310.2296420.2266740.9610.95799.85160.265

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