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- PDB-6vsi: Crystal structure of FKBP12 of Candida auris -

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Basic information

Entry
Database: PDB / ID: 6vsi
TitleCrystal structure of FKBP12 of Candida auris
ComponentsPeptidylprolyl isomerase
KeywordsISOMERASE / FKBP12 / C. auris / pathogenesis
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase Fpr3/Fpr4-like / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidylprolyl isomerase / Peptidylprolyl isomerase
Similarity search - Component
Biological speciesCandida auris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsLi, Z. / Li, H. / Hernandez, G. / LeMaster, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119152 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure and transient dimerization for the FKBP12 protein from the pathogenic fungus Candida auris.
Authors: Bashir, Q. / Li, Z. / Li, H. / LeMaster, D.M. / Hernandez, G.
History
DepositionFeb 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9172
Polymers11,8211
Non-polymers961
Water1,40578
1
A: Peptidylprolyl isomerase
hetero molecules

A: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8354
Polymers23,6432
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area1820 Å2
ΔGint-34 kcal/mol
Surface area10620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.800, 74.800, 72.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

21A-336-

HOH

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Components

#1: Protein Peptidylprolyl isomerase / FK506-binding protein FKBP12


Mass: 11821.423 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida auris (fungus) / Gene: CJJ09_002997 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A5C1DY09, UniProt: A0A2H1A4Z6*PLUS, peptidylprolyl isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.05 Å3/Da / Density % sol: 70 % / Description: long rod
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 2 uL 21.5 mg/mL protein in 20 mM Tris-HCl, pH 8.0, 200 mM sodium chloride + 2 uL 54% saturated ammonium sulfate, 0.1 M HEPES, pH 7.5, 2% isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9796 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.87→37.4 Å / Num. obs: 17303 / % possible obs: 91.89 % / Redundancy: 12.1 % / Biso Wilson estimate: 45.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.021 / Rrim(I) all: 0.074 / Net I/σ(I): 20.8
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 13.3 % / Num. unique obs: 571 / CC1/2: 0.29 / % possible all: 33.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.46 Å52.89 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.7.16phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5HT1

5ht1


Resolution: 1.87→37.4 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.16
RfactorNum. reflection% reflection
Rfree0.2064 723 4.51 %
Rwork0.2018 --
obs0.202 16029 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.28 Å2 / Biso mean: 48.9185 Å2 / Biso min: 33.16 Å2
Refinement stepCycle: final / Resolution: 1.87→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 5 78 916
Biso mean--96.42 54.4 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009865
X-RAY DIFFRACTIONf_angle_d0.9491176
X-RAY DIFFRACTIONf_chiral_restr0.056131
X-RAY DIFFRACTIONf_plane_restr0.005154
X-RAY DIFFRACTIONf_dihedral_angle_d3.921702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.87-2.0140.3392930.3206194259
2.014-2.21670.28721260.28553311100
2.2167-2.53740.27521660.24593289100
2.5374-3.19660.25511540.2358329398
3.1966-37.40.17111840.1686347199

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