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- PDB-3k0o: Room temperature structure of CypA mutant Ser99Thr -

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Basic information

Entry
Database: PDB / ID: 3k0o
TitleRoom temperature structure of CypA mutant Ser99Thr
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 / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / 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 / protein peptidyl-prolyl isomerization / viral release from host cell / Calcineurin activates NFAT / : / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of protein phosphorylation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / peptidyl-prolyl cis-trans isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / negative regulation of protein kinase activity / Assembly Of The HIV Virion / Budding and maturation of HIV virion / neuron differentiation / platelet aggregation / platelet activation / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / unfolded protein binding / Platelet degranulation / protein folding / 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 / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / membrane / 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: 1.55 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 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 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)18,0511
Polymers18,0511
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.438, 60.438, 95.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

21A-269-

HOH

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Components

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


Mass: 18050.529 Da / Num. of mol.: 1 / Mutation: S99T
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.: 119 / 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: 55.89 %
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: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2008
RadiationMonochromator: Kohzu Dual Double Crystal Monochromator (DDCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 29997 / Num. obs: 27237 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.3 % / Rsym value: 0.12 / Net I/σ(I): 21
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 1609 / Rsym value: 0.436 / % possible all: 55

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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: 1.55→35.268 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0.14 / σ(I): 0 / Phase error: 12.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1479 1926 7.34 %phenix.refine
Rwork0.107 ---
obs0.1099 26234 87.63 %-
all-29997 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.565 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0576 Å20 Å2-0 Å2
2--1.0576 Å2-0 Å2
3----2.1151 Å2
Refinement stepCycle: LAST / Resolution: 1.55→35.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 119 1378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111287
X-RAY DIFFRACTIONf_angle_d1.311727
X-RAY DIFFRACTIONf_dihedral_angle_d16.84467
X-RAY DIFFRACTIONf_chiral_restr0.078179
X-RAY DIFFRACTIONf_plane_restr0.006229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5497-1.58840.1952740.1004943X-RAY DIFFRACTION48
1.5884-1.63140.1902960.10031116X-RAY DIFFRACTION58
1.6314-1.67940.2011080.1031414X-RAY DIFFRACTION72
1.6794-1.73360.19451410.09861725X-RAY DIFFRACTION89
1.7336-1.79560.15871370.08921772X-RAY DIFFRACTION91
1.7956-1.86740.13951460.0841806X-RAY DIFFRACTION92
1.8674-1.95240.13171480.08341858X-RAY DIFFRACTION94
1.9524-2.05540.13541490.08481861X-RAY DIFFRACTION95
2.0554-2.18410.13641450.08611899X-RAY DIFFRACTION96
2.1841-2.35270.11891480.08931901X-RAY DIFFRACTION96
2.3527-2.58940.15321610.1081930X-RAY DIFFRACTION97
2.5894-2.96390.15621550.12351959X-RAY DIFFRACTION98
2.9639-3.73360.15421600.11532009X-RAY DIFFRACTION99
3.7336-35.27740.1171580.10742115X-RAY DIFFRACTION99

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