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- PDB-3k0r: Cryogenic structure of CypA mutant Arg55Lys -

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Basic information

Entry
Database: PDB / ID: 3k0r
TitleCryogenic structure of CypA mutant Arg55Lys
ComponentsCyclophilin A
KeywordsISOMERASE / proline isomerase / Acetylation / Cyclosporin / Cytoplasm / Host-virus interaction / Isopeptide bond / Phosphoprotein / Rotamase / Ubl conjugation
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 / peptidylprolyl isomerase / positive regulation of protein secretion / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet activation / 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: 2.424 Å
AuthorsFraser, J.S. / Alber, T.
CitationJournal: Nature / Year: 2009
Title: Hidden alternative structures of proline isomerase essential for catalysis.
Authors: Fraser, J.S. / Clarkson, M.W. / Degnan, S.C. / Erion, R. / Kern, D. / Alber, T.
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.4Oct 13, 2021Group: Database references / Structure summary / Category: database_2 / entity / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclophilin A


Theoretical massNumber of molelcules
Total (without water)18,0081
Polymers18,0081
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.211, 64.211, 93.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18008.488 Da / Num. of mol.: 1 / Mutation: R55K
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.: 59 / 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: 3.09 Å3/Da / Density % sol: 60.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8 M DL-malic acid, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2008
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 8900 / Num. obs: 8900 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rsym value: 0.131 / Net I/σ(I): 16.4
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 853 / Rsym value: 0.572 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceICE/ELVESdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_162)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2cpl

2cpl


Resolution: 2.424→47.803 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.17 / σ(I): 0 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 861 10.13 %phenix.refine
Rwork0.1773 ---
obs0.1834 8496 95.73 %-
all-8900 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.657 Å2 / ksol: 0.436 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5525 Å2-0 Å2-0 Å2
2--3.5525 Å2-0 Å2
3----7.105 Å2
Refinement stepCycle: LAST / Resolution: 2.424→47.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 0 59 2536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191284
X-RAY DIFFRACTIONf_angle_d1.7621722
X-RAY DIFFRACTIONf_dihedral_angle_d18.009466
X-RAY DIFFRACTIONf_chiral_restr0.097178
X-RAY DIFFRACTIONf_plane_restr0.008228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4241-2.5760.30131360.19951174X-RAY DIFFRACTION90
2.576-2.77480.2891310.19091227X-RAY DIFFRACTION93
2.7748-3.0540.25131390.18231238X-RAY DIFFRACTION95
3.054-3.49590.27441490.1791279X-RAY DIFFRACTION98
3.4959-4.40390.20041540.1551328X-RAY DIFFRACTION99
4.4039-47.81240.19431520.15841389X-RAY DIFFRACTION98

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