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- PDB-5hkg: Total chemical synthesis, refolding and crystallographic structur... -

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Basic information

Entry
Database: PDB / ID: 5hkg
TitleTotal chemical synthesis, refolding and crystallographic structure of a fully active immunophilin: calstabin 2 (FKBP12.6).
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1B
KeywordsISOMERASE / Synthetic protein / Refolding / immunophilin
Function / homology
Function and homology information


positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / response to redox state / protein maturation by protein folding / 'de novo' protein folding ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / FK506 binding / positive regulation of axon regeneration / channel regulator activity / smooth muscle contraction / response to vitamin E / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / response to hydrogen peroxide / Stimuli-sensing channels / Z disc / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / signaling receptor binding / membrane / cytosol / cytoplasm
Similarity search - Function
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 FKBP1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSirigu, S. / Huet, T. / Bacchi, M. / Jullian, M. / Fould, B. / Ferry, G. / Vuillard, L. / Chavas, L. / Puget, K. / Nosjean, O. / Boutin, J.A.
CitationJournal: Protein Sci. / Year: 2016
Title: Total chemical synthesis, refolding, and crystallographic structure of fully active immunophilin calstabin 2 (FKBP12.6).
Authors: Bacchi, M. / Jullian, M. / Sirigu, S. / Fould, B. / Huet, T. / Bruyand, L. / Antoine, M. / Vuillard, L. / Ronga, L. / Chavas, L.M. / Nosjean, O. / Ferry, G. / Puget, K. / Boutin, J.A.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 FKBP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9369
Polymers11,6671
Non-polymers1,2698
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-14 kcal/mol
Surface area6180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.200, 48.610, 53.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1B / PPIase FKBP1B / 12.6 kDa FK506-binding protein / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / ...PPIase FKBP1B / 12.6 kDa FK506-binding protein / FKBP-12.6 / FK506-binding protein 1B / FKBP-1B / Immunophilin FKBP12.6 / Rotamase / h-FKBP-12


Mass: 11667.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4 / Production host: synthetic construct (others) / References: UniProt: P68106, 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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16 % PEG 8K, 10% Glycerol, 500 mM KCl, 100 mM Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 19433 / % possible obs: 99.9 % / Redundancy: 17.6 % / Biso Wilson estimate: 18.26 Å2 / Rsym value: 0.045 / Net I/σ(I): 28.08
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 5.25 % / Rsym value: 0.141 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C9H

1c9h


Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.9619 / Cor.coef. Fo:Fc free: 0.9508 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.073 / SU Rfree Cruickshank DPI: 0.068
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 967 5 %RANDOM
Rwork0.1723 ---
obs0.1733 19339 100 %-
Displacement parametersBiso mean: 22.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.2273 Å20 Å20 Å2
2--0.6733 Å20 Å2
3----1.9006 Å2
Refine analyzeLuzzati coordinate error obs: 0.167 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 84 147 1049
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01948HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.191283HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d374SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes21HARMONIC2
X-RAY DIFFRACTIONt_gen_planes145HARMONIC5
X-RAY DIFFRACTIONt_it948HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.39
X-RAY DIFFRACTIONt_other_torsion14.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion131SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1231SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.58 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2222 139 5.01 %
Rwork0.1712 2638 -
all0.1736 2777 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.3976 Å / Origin y: -1.8703 Å / Origin z: -8.3455 Å
111213212223313233
T-0.0405 Å2-0.0029 Å2-0.0053 Å2--0.0284 Å20.0023 Å2---0.0312 Å2
L1.2929 °2-0.5441 °2-0.5416 °2-1.2501 °20.5095 °2--1.6738 °2
S-0.0501 Å °-0.1122 Å °-0.0293 Å °0.007 Å °0.0477 Å °0.021 Å °0.0389 Å °-0.0368 Å °0.0024 Å °
Refinement TLS groupSelection details: { A|* }

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