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- PDB-6lxr: TvCyP2 in apo form 4 -

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Basic information

Entry
Database: PDB / ID: 6lxr
TitleTvCyP2 in apo form 4
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / intracellular membrane-bounded organelle / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsAryal, S. / Chen, C. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2628-B-002-013 Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-2628-M-002-011 Taiwan
CitationJournal: Biomolecules / Year: 2020
Title: N-Terminal Segment of TvCyP2 Cyclophilin fromTrichomonas vaginalisIs Involved in Self-Association, Membrane Interaction, and Subcellular Localization.
Authors: Aryal, S. / Hsu, H.M. / Lou, Y.C. / Chu, C.H. / Tai, J.H. / Hsu, C.H. / Chen, C.
History
DepositionFeb 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)20,1491
Polymers20,1491
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, MONOMERIC PROTEIN
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8820 Å2
Unit cell
Length a, b, c (Å)52.079, 54.539, 59.671
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 20149.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_062520 / Production host: Escherichia coli (E. coli) / References: UniProt: A2DLL4, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M Sodium citrate, 0.2 M Sodium chloride, 0.1 M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.56→26.17 Å / Num. obs: 5340 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.61 Å2 / CC1/2: 0.978 / Net I/σ(I): 18.5
Reflection shellResolution: 2.561→2.653 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 293 / CC1/2: 0.918 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YBA

5yba


Resolution: 2.56→26.17 Å / SU ML: 0.2999 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.7872
RfactorNum. reflection% reflection
Rfree0.2308 533 9.98 %
Rwork0.1677 --
obs0.1741 5340 91.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.84 Å2
Refinement stepCycle: LAST / Resolution: 2.56→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 0 22 1388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771397
X-RAY DIFFRACTIONf_angle_d0.87431879
X-RAY DIFFRACTIONf_chiral_restr0.0591203
X-RAY DIFFRACTIONf_plane_restr0.0065243
X-RAY DIFFRACTIONf_dihedral_angle_d3.5341824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.820.2766960.204864X-RAY DIFFRACTION67.8
2.561-26.170.19791500.14371375X-RAY DIFFRACTION99.8
2.82-3.230.27571450.19971268X-RAY DIFFRACTION98.81
3.23-4.060.23721420.17111300X-RAY DIFFRACTION99.86

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