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- PDB-5wc7: CypA Mutant - I97V S99T C115S -

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Basic information

Entry
Database: PDB / ID: 5wc7
TitleCypA Mutant - I97V S99T C115S
ComponentsPeptidyl-prolyl cis-trans isomerase A
KeywordsISOMERASE / proline isomerase
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / negative regulation of viral life cycle / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / negative regulation of viral life cycle / cell adhesion molecule production / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / endothelial cell activation / negative regulation of stress-activated MAPK cascade / Basigin interactions / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / : / neutrophil chemotaxis / activation of protein kinase B activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of protein phosphorylation / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / platelet activation / neuron differentiation / platelet aggregation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / integrin binding / protein folding / Platelet degranulation / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / focal adhesion / Neutrophil degranulation / apoptotic process / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsFraser, J.S.
CitationJournal: Nat Commun / Year: 2018
Title: Rescue of conformational dynamics in enzyme catalysis by directed evolution.
Authors: Otten, R. / Liu, L. / Kenner, L.R. / Clarkson, M.W. / Mavor, D. / Tawfik, D.S. / Kern, D. / Fraser, J.S.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase A


Theoretical massNumber of molelcules
Total (without water)18,0201
Polymers18,0201
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes at expected molecular weight
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.015, 52.432, 89.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18020.438 Da / Num. of mol.: 1 / Mutation: I97V, S99T, C115S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 MM HEPES PH 7.5, 22% PEG 3350

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2013
RadiationMonochromator: KOHZU DUAL DOUBLE CRYSTAL MONOCHROMATOR (DDCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 1.43→34 Å / Num. obs: 38024 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 16.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.86
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 4 % / Rmerge(I) obs: 0.4822 / Mean I/σ(I) obs: 2.77 / Num. unique obs: 3735 / CC1/2: 0.829 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2801: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cpl

2cpl


Resolution: 1.43→33.982 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1273 1897 4.99 %
Rwork0.1037 --
obs0.1049 38024 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.43→33.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1263 0 0 223 1486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092085
X-RAY DIFFRACTIONf_angle_d1.0062866
X-RAY DIFFRACTIONf_dihedral_angle_d14.218799
X-RAY DIFFRACTIONf_chiral_restr0.086294
X-RAY DIFFRACTIONf_plane_restr0.007397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.46580.22491360.17692549X-RAY DIFFRACTION100
1.4658-1.50540.17591210.13662560X-RAY DIFFRACTION100
1.5054-1.54970.17421380.11742552X-RAY DIFFRACTION100
1.5497-1.59970.14031290.1052551X-RAY DIFFRACTION100
1.5997-1.65690.14341360.08832553X-RAY DIFFRACTION100
1.6569-1.72320.11571330.0812550X-RAY DIFFRACTION100
1.7232-1.80160.11131340.08192557X-RAY DIFFRACTION100
1.8016-1.89660.121320.07842554X-RAY DIFFRACTION100
1.8966-2.01540.10911410.08632569X-RAY DIFFRACTION100
2.0154-2.1710.12791400.08772572X-RAY DIFFRACTION100
2.171-2.38950.10951450.09742599X-RAY DIFFRACTION100
2.3895-2.73510.13441270.10792616X-RAY DIFFRACTION100
2.7351-3.44540.12061260.11252631X-RAY DIFFRACTION99
3.4454-33.99160.12931590.11312714X-RAY DIFFRACTION99

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