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- PDB-5bxj: Complex of the Fk1 domain mutant A19T of FKBP51 with 4-Nitrophenol -

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Basic information

Entry
Database: PDB / ID: 5bxj
TitleComplex of the Fk1 domain mutant A19T of FKBP51 with 4-Nitrophenol
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / cochaperone / FK506 / 4-Nitrophenol
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
P-NITROPHENOL / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.24 Å
AuthorsWu, D. / Tao, X. / Chen, Z. / Han, J. / Jia, W. / Li, X. / Wang, Z. / He, Y.X.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China31300616 China
Fundamental Research Funds of Lanzhou Universitylzujbky-2014- 85 China
Fundamental Research Funds of Lanzhou Universitylzujbky-2013-bt05 China
CitationJournal: J. Hazard. Mater. / Year: 2016
Title: The environmental endocrine disruptor p-nitrophenol interacts with FKBP51, a positive regulator of androgen receptor and inhibits androgen receptor signaling in human cells
Authors: Wu, D. / Tao, X. / Chen, Z.P. / Han, J.T. / Jia, W.J. / Zhu, N. / Li, X. / Wang, Z. / He, Y.X.
History
DepositionJun 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)14,2962
Polymers14,1571
Non-polymers1391
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area6850 Å2
Unit cell
Length a, b, c (Å)42.127, 53.720, 56.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / 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: 14157.275 Da / Num. of mol.: 1 / Fragment: UNP residues 16-140 / Mutation: A19T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-NPO / P-NITROPHENOL / 4-Nitrophenol


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 3350, 0.2 M Ammonium Acetate and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 36610 / % possible obs: 99.2 % / Redundancy: 7 % / Net I/σ(I): 23.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.24→28.024 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1828 5 %
Rwork0.1771 --
obs0.1786 36547 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→28.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 10 137 1123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011006
X-RAY DIFFRACTIONf_angle_d1.3031350
X-RAY DIFFRACTIONf_dihedral_angle_d13.268376
X-RAY DIFFRACTIONf_chiral_restr0.073144
X-RAY DIFFRACTIONf_plane_restr0.007173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2402-1.27380.20791290.17662549X-RAY DIFFRACTION96
1.2738-1.31120.2031440.15842617X-RAY DIFFRACTION100
1.3112-1.35360.19451270.15852664X-RAY DIFFRACTION100
1.3536-1.40190.19211350.15682654X-RAY DIFFRACTION100
1.4019-1.45810.19991350.15852657X-RAY DIFFRACTION100
1.4581-1.52440.17731400.15272653X-RAY DIFFRACTION100
1.5244-1.60480.19791400.15462652X-RAY DIFFRACTION100
1.6048-1.70530.19681430.16042675X-RAY DIFFRACTION100
1.7053-1.8370.17881400.16442679X-RAY DIFFRACTION100
1.837-2.02180.2031480.17092680X-RAY DIFFRACTION100
2.0218-2.31420.20751520.18122690X-RAY DIFFRACTION100
2.3142-2.91520.23011400.19062740X-RAY DIFFRACTION100
2.9152-28.03110.21021550.19192809X-RAY DIFFRACTION98

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