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- PDB-7f2j: Crystal structure of AtFKBP53 FKBD in complex with rapamycin -

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Basic information

Entry
Database: PDB / ID: 7f2j
TitleCrystal structure of AtFKBP53 FKBD in complex with rapamycin
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP53
KeywordsISOMERASE / FKBP / rapamycin / dimerization
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleosome assembly / histone binding / nucleolus / nucleus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase Fpr3/Fpr4-like / Nucleoplasmin-like domain / Nucleoplasmin-like domain / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Peptidyl-prolyl cis-trans isomerase FKBP53
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSingh, A.K. / Saharan, K. / Vasudevan, D.
Funding support India, 2items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2018/000695/PS India
Department of Biotechnology (DBT, India)BT/INF/22/SP22660/2017 India
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Crystal packing reveals rapamycin-mediated homodimerization of an FK506-binding domain.
Authors: Singh, A.K. / Saharan, K. / Baral, S. / Luan, S. / Vasudevan, D.
History
DepositionJun 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP53
B: Peptidyl-prolyl cis-trans isomerase FKBP53
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,71210
Polymers27,2972
Non-polymers2,4158
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-87 kcal/mol
Surface area12020 Å2
Unit cell
Length a, b, c (Å)28.301, 73.949, 61.950
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP53 / PPIase FKBP53 / FK506-binding protein 53 / AtFKBP53 / Immunophilin FKBP53 / Rotamase


Mass: 13648.736 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FKBP53, At4g25340, T30C3_20 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93ZG9, peptidylprolyl isomerase
#2: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Sirolimus


Mass: 914.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H79NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: immunosuppressant, antibiotic*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.36 % / Description: rod-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Bis-Tris (pH 6.5), 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.6→47.01 Å / Num. obs: 32798 / % possible obs: 99.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Net I/σ(I): 11
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1594 / CC1/2: 0.743 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J2M

6j2m


Resolution: 1.6→47.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.01 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20668 1666 5.1 %RANDOM
Rwork0.17662 ---
obs0.17814 31104 99.1 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.08 Å2
2--0.48 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 162 85 2025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0172010
X-RAY DIFFRACTIONr_bond_other_d0.0010.0192023
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.8932723
X-RAY DIFFRACTIONr_angle_other_deg1.0082.6014687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.13519.59298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39615344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5491513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02432
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.391.347945
X-RAY DIFFRACTIONr_mcbond_other3.391.346944
X-RAY DIFFRACTIONr_mcangle_it3.8162.0071183
X-RAY DIFFRACTIONr_mcangle_other3.8192.0081184
X-RAY DIFFRACTIONr_scbond_it12.2671.9681065
X-RAY DIFFRACTIONr_scbond_other12.2621.971066
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.8442.7331534
X-RAY DIFFRACTIONr_long_range_B_refined15.41617.3272059
X-RAY DIFFRACTIONr_long_range_B_other15.43217.2512053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 127 -
Rwork0.228 2273 -
obs--98.16 %

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