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- PDB-5hwc: Aspergillus fumigatus FKBP12 P90G protein bound with FK506 in P21... -

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Basic information

Entry
Database: PDB / ID: 5hwc
TitleAspergillus fumigatus FKBP12 P90G protein bound with FK506 in P212121 space group
ComponentsFK506-binding protein 1A
KeywordsISOMERASE / FKBP12 / prolyl isomerase / FK506
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
8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / FK506-binding protein 1A
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTonthat, N.K. / Schumacher, M.A.
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
DepositionJan 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FK506-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1902
Polymers12,3861
Non-polymers8041
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.010, 51.138, 55.592
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12385.917 Da / Num. of mol.: 1 / Mutation: P90G
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
#2: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#3: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.8M Sodium Phosphate,1.2M Potassium Phosphate, 0.1M Acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 6350 / % possible obs: 90.3 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.057 / Net I/av σ(I): 19.687 / Net I/σ(I): 34.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.05-2.095.20.095199.1
2.09-2.125.40.0861100
2.12-2.165.30.0881100
2.16-2.215.30.079199.7
2.21-2.2630.09126.4
2.26-2.314.30.079167.1
2.31-2.375.50.0731100
2.37-2.435.40.0721100
2.43-2.55.40.0661100
2.5-2.585.40.0621100
2.58-2.685.40.065199.7
2.68-2.785.40.0661100
2.78-2.915.40.0621100
2.91-3.065.40.057199.7
3.06-3.255.40.0531100
3.25-3.514.80.053197
3.51-3.863.90.05142.6
3.86-4.4250.05173.4
4.42-5.565.20.05199.7
5.56-504.70.05199.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→37.636 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.28
RfactorNum. reflection% reflection
Rfree0.226 627 9.92 %
Rwork0.1646 --
obs0.1706 6323 90.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 47.15 Å2 / Biso mean: 12.54 Å2 / Biso min: 2.53 Å2
Refinement stepCycle: final / Resolution: 2.05→37.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms862 0 57 147 1066
Biso mean--18.8 20.24 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007941
X-RAY DIFFRACTIONf_angle_d1.2211276
X-RAY DIFFRACTIONf_chiral_restr0.078141
X-RAY DIFFRACTIONf_plane_restr0.004164
X-RAY DIFFRACTIONf_dihedral_angle_d15.622371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0492-2.25540.23051420.16631303144597
2.2554-2.58170.25521540.17971444159899
2.5817-3.25230.25481760.175615621738100
3.2523-37.64260.19161550.14911387154283

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