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- PDB-5j6e: Structure of disulfide crosslinked A. fumigatus FKBP12(V91C) -

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Basic information

Entry
Database: PDB / ID: 5j6e
TitleStructure of disulfide crosslinked A. fumigatus FKBP12(V91C)
ComponentsFK506-binding protein 1A
KeywordsISOMERASE / FKBP12 / disulfide trapping / crosslinked dimer
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / nucleus / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
FK506-binding protein 1A
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsSchumacher, M.
CitationJournal: Mbio / Year: 2016
Title: Structures of Pathogenic Fungal FKBP12s Reveal Possible Self-Catalysis Function.
Authors: Tonthat, N.K. / Juvvadi, P.R. / Zhang, H. / Lee, S.C. / Venters, R. / Spicer, L. / Steinbach, W.J. / Heitman, J. / Schumacher, M.A.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Data collection / Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FK506-binding protein 1A
B: FK506-binding protein 1A


Theoretical massNumber of molelcules
Total (without water)24,1532
Polymers24,1532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-6 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.887, 136.887, 33.037
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein FK506-binding protein 1A / FKBP / Peptidyl-prolyl cis-trans isomerase / PPIase / Rapamycin-binding protein


Mass: 12076.637 Da / Num. of mol.: 2 / Mutation: V91C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: fpr1A, AFUA_6G12170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WLV6, peptidylprolyl isomerase
Has protein modificationY

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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: 3.7 Å3/Da / Density % sol: 66.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.5 M sodium citrate, sodium cacodylate buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.02→44.807 Å / Num. obs: 10597 / % possible obs: 92.77 % / Redundancy: 2 % / Net I/σ(I): 8.9
Reflection shellHighest resolution: 3.02 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→44.807 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 26.6
RfactorNum. reflection% reflection
Rfree0.2714 589 10.06 %
Rwork0.2097 --
obs0.2161 10597 92.77 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 0.001 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso max: 135.89 Å2 / Biso mean: 19.35 Å2 / Biso min: 5.01 Å2
Baniso -1Baniso -2Baniso -3
1--8.9103 Å20 Å2-0 Å2
2---8.9103 Å20 Å2
3----13.448 Å2
Refinement stepCycle: final / Resolution: 3.2→44.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1692 0 0 0 1692
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111731
X-RAY DIFFRACTIONf_angle_d2.172340
X-RAY DIFFRACTIONf_chiral_restr0.095252
X-RAY DIFFRACTIONf_plane_restr0.01310
X-RAY DIFFRACTIONf_dihedral_angle_d15.889644
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2005-3.34610.31181460.26021277142398
3.3461-3.52240.32551410.24731244138597
3.5224-3.7430.32111340.26181226136097
3.743-4.03190.30871430.22341233137696
4.0319-4.43730.26011320.16161191132394
4.4373-5.07860.18271280.1481176130491
5.0786-6.39550.22971140.19761142125688
6.3955-44.81120.23461280.19241042117082

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