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- PDB-3k0n: Room temperature structure of CypA -

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Basic information

Entry
Database: PDB / ID: 3k0n
TitleRoom temperature structure of CypA
ComponentsCyclophilin A
KeywordsISOMERASE / proline isomerase / Cyclosporin / Host-virus interaction / Isopeptide bond / Phosphoprotein / Rotamase
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / leukocyte chemotaxis / virion binding / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / 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 / negative regulation of protein phosphorylation / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / Calcineurin activates NFAT / activation of protein kinase B activity / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein kinase activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of protein secretion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Assembly Of The HIV Virion / positive regulation of NF-kappaB transcription factor activity / Budding and maturation of HIV virion / platelet activation / platelet aggregation / integrin binding / positive regulation of protein phosphorylation / neuron differentiation / SARS-CoV-1 activates/modulates innate immune responses / unfolded protein binding / Platelet degranulation / protein folding / cellular response to oxidative stress / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / positive regulation of MAPK cascade / focal adhesion / apoptotic process / Neutrophil degranulation / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / cytoplasm / cytosol
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: 1.391 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 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 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

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Assembly

Deposited unit
A: Cyclophilin A


Theoretical massNumber of molelcules
Total (without water)18,0371
Polymers18,0371
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.096, 52.592, 89.249
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 Cyclophilin A / Peptidyl-prolyl cis-trans isomerase A / PPIase A / Rotamase A / Cyclosporin A-binding protein


Mass: 18036.504 Da / Num. of mol.: 1
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.: 132 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 22% PEG 3350, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.115831 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 31, 2008
RadiationMonochromator: Kohzu Dual Double Crystal Monochromator (DDCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115831 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. all: 41498 / Num. obs: 39216 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.101 / Net I/σ(I): 21
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 3743 / Rsym value: 0.507 / % possible all: 87

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Processing

Software
NameVersionClassification
HKL-2000data 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: 1.391→33.334 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 14.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1596 1900 4.84 %phenix.refine
Rwork0.1222 ---
obs0.124 39216 94.5 %-
all-41498 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.954 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.784 Å20 Å2-0 Å2
2--1.725 Å2-0 Å2
3----0.9409 Å2
Refinement stepCycle: LAST / Resolution: 1.391→33.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1248 0 0 132 1380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111564
X-RAY DIFFRACTIONf_angle_d1.2642118
X-RAY DIFFRACTIONf_dihedral_angle_d15.948576
X-RAY DIFFRACTIONf_chiral_restr0.076223
X-RAY DIFFRACTIONf_plane_restr0.008281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3909-1.42570.27751110.17832073X-RAY DIFFRACTION76
1.4257-1.46420.22561250.14782394X-RAY DIFFRACTION86
1.4642-1.50730.19311300.12622476X-RAY DIFFRACTION89
1.5073-1.5560.19451260.112586X-RAY DIFFRACTION92
1.556-1.61160.1541330.10632607X-RAY DIFFRACTION95
1.6116-1.67610.17911320.09912682X-RAY DIFFRACTION95
1.6761-1.75240.14921380.10512714X-RAY DIFFRACTION97
1.7524-1.84480.15611370.10182734X-RAY DIFFRACTION98
1.8448-1.96030.1511430.10082772X-RAY DIFFRACTION99
1.9603-2.11170.13351420.10342784X-RAY DIFFRACTION99
2.1117-2.32410.14781410.1092810X-RAY DIFFRACTION99
2.3241-2.66030.17171440.12532828X-RAY DIFFRACTION99
2.6603-3.35120.15631450.13382866X-RAY DIFFRACTION99
3.3512-33.34350.13471530.11962990X-RAY DIFFRACTION99

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