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- PDB-3k0m: Cryogenic structure of CypA -

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Basic information

Entry
Database: PDB / ID: 3k0m
TitleCryogenic 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: 1.25 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
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.419, 51.741, 88.639
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.: 269 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.953695 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2007
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953695 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 52646 / Num. obs: 54771 / % possible obs: 96.12 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rsym value: 0.042 / Net I/σ(I): 38.3
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 5385 / Rsym value: 0.564 / % possible all: 89.8

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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: 1.25→33.659 Å / SU ML: 0.11 / σ(F): 0.12 / Phase error: 12.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1492 2637 5.01 %phenix.refine
Rwork0.1294 ---
obs0.1305 52646 96.12 %-
all-52646 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.403 Å2 / ksol: 0.435 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8217 Å20 Å20 Å2
2--0.957 Å20 Å2
3----0.1354 Å2
Refinement stepCycle: LAST / Resolution: 1.25→33.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1251 0 0 269 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011428
X-RAY DIFFRACTIONf_angle_d1.3071925
X-RAY DIFFRACTIONf_dihedral_angle_d14.858524
X-RAY DIFFRACTIONf_chiral_restr0.082194
X-RAY DIFFRACTIONf_plane_restr0.006260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.27270.19781390.13822373X-RAY DIFFRACTION88
1.2727-1.29720.18411080.13032437X-RAY DIFFRACTION90
1.2972-1.32370.17321430.11972471X-RAY DIFFRACTION91
1.3237-1.35250.16891080.11612508X-RAY DIFFRACTION93
1.3525-1.3840.15311280.11922523X-RAY DIFFRACTION93
1.384-1.41860.13551500.1122554X-RAY DIFFRACTION95
1.4186-1.45690.13981460.10662601X-RAY DIFFRACTION96
1.4569-1.49980.1451480.10092576X-RAY DIFFRACTION96
1.4998-1.54820.14261360.09672627X-RAY DIFFRACTION97
1.5482-1.60350.11841560.1012632X-RAY DIFFRACTION97
1.6035-1.66770.13591260.10072664X-RAY DIFFRACTION98
1.6677-1.74360.11971280.10652675X-RAY DIFFRACTION98
1.7436-1.83560.13741400.10822698X-RAY DIFFRACTION98
1.8356-1.95050.15361370.11522706X-RAY DIFFRACTION99
1.9505-2.10110.15641300.11422755X-RAY DIFFRACTION99
2.1011-2.31250.12641400.11812744X-RAY DIFFRACTION99
2.3125-2.6470.1551480.13412769X-RAY DIFFRACTION99
2.647-3.33450.12821580.13992778X-RAY DIFFRACTION99
3.3345-33.67170.16371680.15582918X-RAY DIFFRACTION99

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