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- PDB-1yw5: Peptidyl-prolyl isomerase ESS1 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 1yw5
TitlePeptidyl-prolyl isomerase ESS1 from Candida albicans
Componentspeptidyl prolyl cis/trans isomerase
KeywordsISOMERASE / WW-domain / PPIase domain / ordered linker
Function / homology
Function and homology information


positive regulation of rDNA heterochromatin formation / filamentous growth of a population of unicellular organisms in response to heat / filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth of a population of unicellular organisms in response to starvation / fungal biofilm matrix / filamentous growth / termination of RNA polymerase II transcription / RNA polymerase II complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of ubiquitin-dependent protein catabolic process ...positive regulation of rDNA heterochromatin formation / filamentous growth of a population of unicellular organisms in response to heat / filamentous growth of a population of unicellular organisms in response to biotic stimulus / filamentous growth of a population of unicellular organisms in response to starvation / fungal biofilm matrix / filamentous growth / termination of RNA polymerase II transcription / RNA polymerase II complex binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of ubiquitin-dependent protein catabolic process / cellular response to starvation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cellular response to heat / negative regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / Chitinase A; domain 3 ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / : / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / Chitinase A; domain 3 / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Single Sheet / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.6 Å
AuthorsLi, Z. / Li, H. / Devasahayam, G. / Gemmill, T. / Chaturvedi, V. / Hanes, S.D. / Van Roey, P.
CitationJournal: Biochemistry / Year: 2005
Title: The Structure of the Candida albicans Ess1 Prolyl Isomerase Reveals a Well-Ordered Linker that Restricts Domain Mobility
Authors: Li, Z. / Li, H. / Devasahayam, G. / Gemmill, T. / Chaturvedi, V. / Hanes, S.D. / Van Roey, P.
History
DepositionFeb 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: peptidyl prolyl cis/trans isomerase


Theoretical massNumber of molelcules
Total (without water)19,8831
Polymers19,8831
Non-polymers00
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.840, 59.520, 44.860
Angle α, β, γ (deg.)90.00, 91.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein peptidyl prolyl cis/trans isomerase


Mass: 19883.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(31)
References: UniProt: Q9C475, UniProt: Q59KZ2*PLUS, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, MONOBASIC PHOSPHATE, AMMONIUM ACETATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 5, 2002 / Details: Yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 20643 / Num. obs: 20577 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 28.4
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 2.5 / % possible all: 91

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→26.67 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 504444.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1991 9.9 %RANDOM
Rwork0.2 ---
obs0.2 20204 97.1 %-
all-20561 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1179 Å2 / ksol: 0.334435 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å2-2.74 Å2
2---1.67 Å20 Å2
3---0.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→26.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1400 0 0 369 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.862.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.436 273 9.1 %
Rwork0.421 2730 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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