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- PDB-5hwb: Aspergillus fumigatus FKBP12 apo protein in P212121 space group -

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Basic information

Entry
Database: PDB / ID: 5hwb
TitleAspergillus fumigatus FKBP12 apo protein in P212121 space group
ComponentsFK506-binding protein 1A
KeywordsISOMERASE / FKBP12 / prolyl isomerase / FK506
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / nucleus / cytoplasm / cytosol
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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 / Resolution: 2.306 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 28, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,5249
Polymers24,8522
Non-polymers6727
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-103 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.799, 50.834, 102.996
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: 12425.979 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2M Ammonium Sulfate, 0.1 Tris-HCl pH 7.0 and 0.2 Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 10718 / % possible obs: 98.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.069 / Net I/av σ(I): 18.528 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.342.60.366191.2
2.34-2.383.10.371196.5
2.38-2.433.70.396198.5
2.43-2.4840.388199.4
2.48-2.534.40.289199.2
2.53-2.593.60.349199.8
2.59-2.662.90.166197.8
2.66-2.734.30.2291100
2.73-2.814.60.1691100
2.81-2.94.70.1381100
2.9-34.60.1091100
3-3.124.70.0891100
3.12-3.264.70.073199.8
3.26-3.444.70.064199.8
3.44-3.654.70.056199.6
3.65-3.934.70.052199.8
3.93-4.334.70.049199.3
4.33-4.954.60.042199.1
4.95-6.244.60.044198.4
6.24-504.30.035196.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.306→45.584 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.06
RfactorNum. reflection% reflection
Rfree0.2584 1068 10.02 %
Rwork0.2051 --
obs0.2105 10660 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.62 Å2 / Biso mean: 33.83 Å2 / Biso min: 15.45 Å2
Refinement stepCycle: final / Resolution: 2.306→45.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 35 115 1856
Biso mean--47.28 35.69 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021773
X-RAY DIFFRACTIONf_angle_d0.7152406
X-RAY DIFFRACTIONf_chiral_restr0.027257
X-RAY DIFFRACTIONf_plane_restr0.003313
X-RAY DIFFRACTIONf_dihedral_angle_d12.747640
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 (%)
2.3065-2.41140.34371190.26261068118789
2.4114-2.53860.34481320.26671188132099
2.5386-2.69760.35081310.27131166129798
2.6976-2.90580.32851340.265812071341100
2.9058-3.19820.32121350.232112231358100
3.1982-3.66080.21851350.200512131348100
3.6608-4.61150.19361380.15911238137699
4.6115-45.59310.2361440.17611289143398

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