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- PDB-1n1a: Crystal Structure of the N-terminal domain of human FKBP52 -

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Basic information

Entry
Database: PDB / ID: 1n1a
TitleCrystal Structure of the N-terminal domain of human FKBP52
ComponentsFKBP52
KeywordsISOMERASE / FKBP52 / the N-terminal domain
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 / nuclear glucocorticoid receptor binding / copper ion transport / protein-containing complex localization / FK506 binding / androgen receptor signaling pathway ...steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / nuclear glucocorticoid receptor binding / copper ion transport / protein-containing complex localization / FK506 binding / androgen receptor signaling pathway / negative regulation of microtubule polymerization / Attenuation phase / axonal growth cone / : / heat shock protein binding / embryo implantation / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / 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 / Estrogen-dependent gene expression / Potential therapeutics for SARS / microtubule / 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 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. ...Tetratricopeptide repeat 2 / Tetratricopeptide repeat / : / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLi, P. / Ding, Y. / Wu, B. / Shu, C. / Shen, B. / Rao, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the N-terminal domain of human FKBP52.
Authors: Li, P. / Ding, Y. / Wu, B. / Shu, C. / Shen, B. / Rao, Z.
History
DepositionOct 16, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 8, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: FKBP52
B: FKBP52


Theoretical massNumber of molelcules
Total (without water)30,6732
Polymers30,6732
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-15 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.805, 58.362, 70.904
Angle α, β, γ (deg.)90.00, 98.31, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer in the asymmetric unit

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Components

#1: Protein FKBP52 / FK506-binding protein 4


Mass: 15336.519 Da / Num. of mol.: 2 / Fragment: the N-terminal fragment (1-140)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP4 / Plasmid: PET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q02790, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.85 Å3/Da / Density % sol: 33.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, Ammonium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMsodium cacodylate1drop
220-30 mg/mlprotein1drop
32.0 Mammonium sulfate1reservoir
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2001 / Details: mirrors
RadiationMonochromator: CuKa / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 26262 / Num. obs: 26259 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 17.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 9.3 / Num. unique all: 8929 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 8929 / Num. measured all: 26262
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 99.9 % / Num. unique obs: 889

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FKJ

1fkj


Resolution: 2.4→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 822 -Random
Rwork0.204 ---
all0.219 7867 --
obs0.219 7790 99 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.864 Å20 Å2-14.009 Å2
2--13.27 Å20 Å2
3----6.406 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 0 55 1921
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2571.5
X-RAY DIFFRACTIONc_mcangle_it2.0562
X-RAY DIFFRACTIONc_scbond_it1.8892
X-RAY DIFFRACTIONc_scangle_it2.6332.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.3

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