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- PDB-1q1c: Crystal structure of N(1-260) of human FKBP52 -

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Basic information

Entry
Database: PDB / ID: 1q1c
TitleCrystal structure of N(1-260) of human FKBP52
ComponentsFK506-binding protein 4
KeywordsISOMERASE / Rotamase / TPR repeat / Nuclear protein / Phosphorylation
Function / homology
Function and homology information


steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / copper ion transport / nuclear glucocorticoid receptor binding / protein-containing complex localization / negative regulation of microtubule polymerization / FK506 binding ...steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / copper ion transport / nuclear glucocorticoid receptor binding / protein-containing complex localization / negative regulation of microtubule polymerization / FK506 binding / androgen receptor signaling pathway / Attenuation phase / axonal growth cone / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / embryo implantation / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / tau protein binding / protein folding / negative regulation of neuron projection development / protein-macromolecule adaptor activity / microtubule / Estrogen-dependent gene expression / Potential therapeutics for SARS / neuronal cell body / GTP binding / perinuclear region of cytoplasm / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat 2 / 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 ...Tetratricopeptide repeat 2 / 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
Peptidyl-prolyl cis-trans isomerase FKBP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, B. / Li, P. / Lou, Z. / Ding, Y. / Shu, C. / Shen, B. / Rao, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: 3D structure of human FK506-binding protein 52: Implications for the assembly of the glucocorticoid receptor/Hsp90/immunophilin heterocomplex
Authors: Wu, B. / Li, P. / Liu, Y. / Lou, Z. / Ding, Y. / Shu, C. / Ye, S. / Bartlam, M. / Shen, B. / Rao, Z.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: FK506-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8187
Polymers31,3651
Non-polymers4536
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.829, 42.218, 79.065
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FK506-binding protein 4 / Peptidyl-prolyl cis-trans isomerase / PPiase / Rotamase / p59 protein / HSP binding immunophilin / ...Peptidyl-prolyl cis-trans isomerase / PPiase / Rotamase / p59 protein / HSP binding immunophilin / HBI / FKBP52 protein / 52 kDa FK506 binding protein / FKBP59 / N(1-260) OF FKBP52


Mass: 31365.424 Da / Num. of mol.: 1 / Fragment: RESIDUES (-19)-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q02790, peptidylprolyl isomerase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.69 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG6000, Tris, DMSO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.28 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 25105 / Num. obs: 23816 / % possible obs: 96.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.9→1.97 Å / % possible all: 98.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 2362 RANDOM
Rwork0.208 --
all0.211 25105 -
obs0.211 23816 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 24 210 2116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d

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