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- PDB-3kz7: C-terminal domain of Murine FKBP25 rapamycin complex -

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Basic information

Entry
Database: PDB / ID: 3kz7
TitleC-terminal domain of Murine FKBP25 rapamycin complex
ComponentsFK506-binding protein 3
KeywordsISOMERASE/INHIBITOR / FKPB PPiase RAPAMYCIN / Isomerase / Nucleus / Phosphoprotein / Rotamase / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase FKBP3 / FKBP3, basic tilted helix bundle domain / Basic tilted helix bundle domain / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Peptidyl-prolyl cis-trans isomerase FKBP3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsStura, E.A. / Galat, A.
CitationJournal: Int.J.Biol.Macromol. / Year: 2014
Title: Diversified targets of FKBP25 and its complex with rapamycin.
Authors: Galat, A. / Thai, R. / Stura, E.A.
History
DepositionDec 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Aug 20, 2014Group: Database references
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: FK506-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1992
Polymers13,2841
Non-polymers9141
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.649, 85.649, 53.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FK506-binding protein 3 / Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase / 25 kDa FKBP / FKBP-25 / Rapamycin- ...Peptidyl-prolyl cis-trans isomerase / PPIase / Rotamase / 25 kDa FKBP / FKBP-25 / Rapamycin-selective 25 kDa immunophilin


Mass: 13284.337 Da / Num. of mol.: 1 / Fragment: FK506-like binding domain (UNP residues 106-224)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fkbp25, Fkbp3 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q62446, peptidylprolyl isomerase
#2: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


Mass: 914.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H79NO13 / Comment: immunosuppressant, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 3.66 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.4M ammonium sulfate, 120mM Na citrate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2005 / Details: Horizontally bent Ge(220)
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.68→68 Å / Num. all: 23057 / Num. obs: 23011 / % possible obs: 99.8 % / Observed criterion σ(F): 5.26 / Observed criterion σ(I): 1.2 / Redundancy: 14 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 6.5
Reflection shellResolution: 1.88→1.88 Å / Redundancy: 14 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 12.8 / Rsym value: 0.12 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PBK

1pbk


Resolution: 1.95→38.303 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.93 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 740 4.99 %RANDOM
Rwork0.175 ---
all0.1773 ---
obs0.1773 14836 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.656 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9916 Å20 Å20 Å2
2---0.9916 Å20 Å2
3---1.9832 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 65 171 1172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061057
X-RAY DIFFRACTIONf_angle_d1.0751439
X-RAY DIFFRACTIONf_dihedral_angle_d16.972430
X-RAY DIFFRACTIONf_chiral_restr0.073162
X-RAY DIFFRACTIONf_plane_restr0.004180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9501-2.10060.21911610.18452755100
2.1006-2.3120.24551490.17632774100
2.312-2.64650.2661380.19032810100
2.6465-3.3340.22981460.1772832100
3.334-38.31060.1921460.1653292598

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