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- PDB-6lxq: TvCyP2 in apo form 3 -

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Basic information

Entry
Database: PDB / ID: 6lxq
TitleTvCyP2 in apo form 3
ComponentsPeptidyl-prolyl cis-trans isomeraseProlyl 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
PHOSPHATE ION / Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,17712
Polymers20,1491
Non-polymers1,02711
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MONOMERIC PROTEIN
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-29 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.307, 54.643, 59.916
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / Prolyl 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: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M di-Ammonium hydrogen Phosphate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→27.15 Å / Num. obs: 14941 / % possible obs: 99.7 % / Redundancy: 4.6 % / CC1/2: 0.981 / Net I/σ(I): 23.9
Reflection shellResolution: 1.855→1.921 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1076 / CC1/2: 0.924 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YBA

5yba


Resolution: 1.85→27.15 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.89
RfactorNum. reflection% reflection
Rfree0.1827 2401 9.96 %
Rwork0.1463 --
obs0.15 14941 82.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.33 Å2 / Biso mean: 24.2913 Å2 / Biso min: 5.77 Å2
Refinement stepCycle: final / Resolution: 1.85→27.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 61 106 1541
Biso mean--64.08 35.41 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.855-1.89270.2141640.175356137
1.8927-1.93380.2369790.169172446
1.9338-1.97880.1839880.165184355
1.9788-2.02830.19081060.155595761
2.0283-2.08310.18311260.1444109771
2.0831-2.14440.20061280.1491118577
2.1444-2.21360.19071480.1412128283
2.2136-2.29270.19361480.1381133388
2.2927-2.38440.20061670.1405144892
2.3844-2.49290.1911490.1437149597
2.4929-2.62420.20441690.1521530100
2.6242-2.78860.17891760.15071543100
2.7886-3.00370.19141710.14541540100
3.0037-3.30560.17721670.14031540100
3.3056-3.78310.16531720.12331538100
3.7831-4.76320.1541720.13471542100
4.7632-29.9580.19341710.18141546100
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)
11.5989-0.092-0.10310.0501-0.1890.450.55130.0567-0.3881-0.5824-0.32680.08390.40360.25450.32190.21910.11660.0090.20790.00360.105-4.989-2.3562-5.5399
20.6654-0.07730.35830.3657-0.26420.7597-0.13460.2273-0.6294-0.2029-0.0203-0.16990.45280.2620.03190.19920.00430.05690.0413-0.02350.2364-12.474-19.274412.5797
30.2931-0.08730.24750.0374-0.07670.3091-0.1290.2732-0.1041-0.18570.0628-0.13710.12990.4409-0.01720.1672-0.01880.01750.18130.02140.1429-6.8121-6.27766.7747
40.22730.15130.12660.61950.08750.548-0.0397-0.03860.00370.01250.0563-0.2710.07810.59780.080.11940.0275-0.02330.2561-0.00270.1764-1.0182-8.013120.1212
50.1299-0.02630.04910.05190.10110.16050.05130.0422-0.12330.1651-0.07040.06050.163-0.0011-0.01950.1220.0151-0.01740.1160.00730.138-13.2586-12.180621.0954
60.10660.1173-0.12210.1473-0.11050.09980.0176-0.08350.05240.0408-0.01410.13330.0818-0.1053-00.1060.01380.00620.1228-0.01160.109-17.9131-7.639222.0634
70.3559-0.1228-0.25690.1196-0.0720.2187-0.00060.07560.11570.01240.0071-0.1209-0.19580.28130.00040.1476-0.0432-0.0270.1227-0.0060.1316-8.98971.266115.0856
80.6993-0.1941-0.06020.4055-0.46820.39740.01250.03260.05790.0220.0184-0.0017-0.1010.00840.03120.0928-0.00390.00150.0543-0.00240.0729-15.0406-0.480613.8062
90.2662-0.15420.32010.3584-0.02950.50880.08470.0364-0.0993-0.3690.00640.170.0888-0.24550.16680.1754-0.0294-0.03890.1268-0.00220.1743-22.7562-14.69539.5498
100.31120.0046-0.05750.0063-0.0130.01730.01690.0263-0.02910.1469-0.12310.4466-0.0126-0.1871-0.0030.1838-0.00560.05050.1544-0.02910.2345-27.6056-12.875121.0665
110.92080.24251.01151.07860.29891.2367-0.01470.5371-0.3831-0.43770.0375-0.14740.46140.3240.31290.24840.06810.04320.260700.2127-5.6849-17.422311.4727
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 16 )A5 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 31 )A17 - 31
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 42 )A32 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 64 )A43 - 64
5X-RAY DIFFRACTION5chain 'A' and (resid 65 through 77 )A65 - 77
6X-RAY DIFFRACTION6chain 'A' and (resid 78 through 94 )A78 - 94
7X-RAY DIFFRACTION7chain 'A' and (resid 95 through 120 )A95 - 120
8X-RAY DIFFRACTION8chain 'A' and (resid 121 through 155 )A121 - 155
9X-RAY DIFFRACTION9chain 'A' and (resid 156 through 165 )A156 - 165
10X-RAY DIFFRACTION10chain 'A' and (resid 166 through 175 )A166 - 175
11X-RAY DIFFRACTION11chain 'A' and (resid 176 through 187 )A176 - 187

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