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- PDB-6bta: CypA Mutant - S99T C115S -

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Basic information

Entry
Database: PDB / ID: 6bta
TitleCypA Mutant - 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 / 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 / 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 / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / negative regulation of protein phosphorylation / 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 / 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 / negative regulation of protein kinase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / Assembly Of The HIV Virion / Budding and maturation of HIV virion / platelet activation / platelet aggregation / neuron differentiation / positive regulation of NF-kappaB transcription factor activity / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / unfolded protein binding / Platelet degranulation / protein folding / positive regulation of protein phosphorylation / 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 / 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: 1.5 Å
AuthorsFraser, J.S. / Kenner, L.R. / Liu, L.
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
DepositionDec 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)18,0341
Polymers18,0341
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.970, 52.540, 89.270
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: 18034.465 Da / Num. of mol.: 1 / Mutation: 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.: 160 / 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: 55.97 %
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: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2013
RadiationMonochromator: KOHZU DUAL DOUBLE CRYSTAL MONOCHROMATOR (DDCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.45→34.02 Å / Num. obs: 36477 / % possible obs: 99.6 % / Redundancy: 4 % / Net I/σ(I): 13.7
Reflection shellResolution: 1.45→1.49 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2cpl

2cpl


Resolution: 1.5→34.017 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.12
RfactorNum. reflection% reflection
Rfree0.146 1697 5.14 %
Rwork0.1312 --
obs0.132 32996 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→34.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 160 1419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081948
X-RAY DIFFRACTIONf_angle_d0.9812659
X-RAY DIFFRACTIONf_dihedral_angle_d9.4761193
X-RAY DIFFRACTIONf_chiral_restr0.13278
X-RAY DIFFRACTIONf_plane_restr0.006360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.54420.24791440.25172576X-RAY DIFFRACTION100
1.5442-1.5940.23091340.21822564X-RAY DIFFRACTION100
1.594-1.6510.2121450.19212574X-RAY DIFFRACTION100
1.651-1.71710.18411540.16842546X-RAY DIFFRACTION100
1.7171-1.79520.1711370.1442596X-RAY DIFFRACTION100
1.7952-1.88980.14491280.12822604X-RAY DIFFRACTION100
1.8898-2.00820.1461310.1252589X-RAY DIFFRACTION100
2.0082-2.16330.14181440.1172607X-RAY DIFFRACTION100
2.1633-2.38090.16011290.11652615X-RAY DIFFRACTION100
2.3809-2.72530.12751300.12542643X-RAY DIFFRACTION100
2.7253-3.43310.13591460.1272637X-RAY DIFFRACTION99
3.4331-34.02560.12961750.11772748X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40650.38380.46980.79950.27631.09970.01420.1212-0.1009-0.1525-0.02760.05060.1416-0.22910.04260.1316-0.02490.00510.1351-0.00750.1336-7.9766.0827-19.079
20.4209-0.0438-0.50450.31110.01050.43370.0247-0.00910.0467-0.00540.051-0.0158-0.0598-0.00670.01830.12090.0085-0.00570.11130.0110.1254-0.404713.2703-15.1544
30.06140.09490.02250.11160.08920.37080.07510.00090.14570.0138-0.02830.1007-0.3497-0.1332-0.00620.17960.03940.02180.13630.01590.177-9.181721.3125-12.5071
40.6875-0.1106-0.39590.177-0.03261.12170.066-0.1092-0.03570.0332-0.04950.03440.0767-0.00460.050.0927-0.02130.00710.09290.00470.0936-6.84648.201-4.6011
50.31580.09220.06390.2055-0.21350.201-0.0184-0.0352-0.0217-0.04070.00740.03940.2156-0.11720.00040.1234-0.03010.010.1002-0.00530.1015-7.27974.7144-7.9187
60.05220.113-0.03810.0370.01850.13270.0260.02380.08830.13960.04420.03260.28730.17040.01120.20930.03450.00230.1568-0.04080.15157.17212.3449-17.0522
70.0363-0.2011-0.22820.4210.1520.78170.05650.07520.0312-0.11290.0223-0.0458-0.0310.17370.01870.1298-0.02580.00830.1562-0.0080.13634.858711.8695-18.6008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 122 )
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 135 )
6X-RAY DIFFRACTION6chain 'A' and (resid 136 through 145 )
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 165 )

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