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- PDB-4r0x: Allosteric coupling of conformational transitions in the FK1 doma... -

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Basic information

Entry
Database: PDB / ID: 4r0x
TitleAllosteric coupling of conformational transitions in the FK1 domain of FKBP51 near the site of steroid receptor interaction
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
Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLeMaster, D.M. / Mustafi, S.M. / Brecher, M. / Zhang, J. / Heroux, A. / Li, H.M. / Hernandez, G.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Coupling of Conformational Transitions in the N-terminal Domain of the 51-kDa FK506-binding Protein (FKBP51) Near Its Site of Interaction with the Steroid Receptor Proteins.
Authors: LeMaster, D.M. / Mustafi, S.M. / Brecher, M. / Zhang, J. / Heroux, A. / Li, H. / Hernandez, G.
History
DepositionAug 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2May 27, 2015Group: Data collection
Revision 1.3Jul 22, 2015Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)13,4871
Polymers13,4871
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase FKBP5

A: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)26,9752
Polymers26,9752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area960 Å2
ΔGint-9 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.435, 31.990, 57.435
Angle α, β, γ (deg.)90.00, 119.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

21A-362-

HOH

31A-368-

HOH

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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: 13487.483 Da / Num. of mol.: 1 / Fragment: UNP residues 20-140 / Mutation: K120G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIG6, FKBP5, FKBP51 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 26% PEG 3350, 0.1 M HEPES, pH 7.5, 0.2 M ammonium acetate, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2014
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→27.455 Å / Num. all: 32435 / Num. obs: 32439 / % possible obs: 93.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 34.4
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.2 / Num. unique all: 868 / Rsym value: 0.36 / % possible all: 50.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3O5E

3o5e


Resolution: 1.2→27.45 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1674 2000 6.17 %RANDOM
Rwork0.1589 ---
obs0.1594 32435 93.26 %-
all-32435 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms947 0 0 193 1140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006973
X-RAY DIFFRACTIONf_angle_d1.081305
X-RAY DIFFRACTIONf_dihedral_angle_d11.032370
X-RAY DIFFRACTIONf_chiral_restr0.043137
X-RAY DIFFRACTIONf_plane_restr0.006169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22970.2483820.24731258X-RAY DIFFRACTION54
1.2297-1.2630.21081050.2071579X-RAY DIFFRACTION69
1.263-1.30020.20371290.19231975X-RAY DIFFRACTION86
1.3002-1.34210.20231480.17662248X-RAY DIFFRACTION97
1.3421-1.39010.18671510.17162305X-RAY DIFFRACTION100
1.3901-1.44570.15011530.1632326X-RAY DIFFRACTION100
1.4457-1.51150.17741530.16412323X-RAY DIFFRACTION100
1.5115-1.59120.16261530.15692323X-RAY DIFFRACTION100
1.5912-1.69090.1771520.15552327X-RAY DIFFRACTION100
1.6909-1.82140.17351530.16052325X-RAY DIFFRACTION100
1.8214-2.00470.16941530.15062325X-RAY DIFFRACTION100
2.0047-2.29460.17521540.14912347X-RAY DIFFRACTION100
2.2946-2.89050.17371550.16892357X-RAY DIFFRACTION100
2.8905-27.46190.14421590.14832417X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -16.8166 Å / Origin y: 3.339 Å / Origin z: 11.0126 Å
111213212223313233
T0.0982 Å20.0016 Å2-0.0096 Å2-0.0913 Å20.0024 Å2--0.0848 Å2
L0.5555 °2-0.2661 °2-0.1018 °2-0.5586 °20.1837 °2--1.0134 °2
S-0.0203 Å °-0.1321 Å °-0.0081 Å °0.0795 Å °0.0305 Å °0.0076 Å °-0.0633 Å °-0.0194 Å °-0.0059 Å °
Refinement TLS groupSelection details: ALL

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