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- PDB-6gmp: CRYSTAL STRUCTURE OF THE PPIASE DOMAIN OF TBPAR42 -

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Basic information

Entry
Database: PDB / ID: 6gmp
TitleCRYSTAL STRUCTURE OF THE PPIASE DOMAIN OF TBPAR42
ComponentsPARVULIN 42
KeywordsISOMERASE / PPIASE
Function / homology
Function and homology information


maintenance of RNA location / protein serine/threonine phosphatase inhibitor activity / negative regulation of protein dephosphorylation / miRNA processing / peptidyl-prolyl cis-trans isomerase activity / mRNA splicing, via spliceosome / nuclear speck / mRNA binding / nucleus
Similarity search - Function
PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / Chitinase A; domain 3 - #40 / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Chitinase A; domain 3 ...PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / Chitinase A; domain 3 - #40 / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Chitinase A; domain 3 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHoenig, D. / Rute, A. / Hofmann, E. / Bayer, P. / Gasper, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationResearch Training Group 1431 Germany
CitationJournal: Biomolecules / Year: 2019
Title: Structural Analysis of the 42 kDa Parvulin ofTrypanosoma brucei.
Authors: Rehic, E. / Hoenig, D. / Kamba, B.E. / Goehring, A. / Hofmann, E. / Gasper, R. / Matena, A. / Bayer, P.
History
DepositionMay 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.country / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 1, 2024Group: 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: PARVULIN 42


Theoretical massNumber of molelcules
Total (without water)13,6761
Polymers13,6761
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.640, 69.960, 102.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

21A-485-

HOH

31A-521-

HOH

41A-528-

HOH

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Components

#1: Protein PARVULIN 42


Mass: 13676.392 Da / Num. of mol.: 1 / Fragment: PPIASE DOMAIN (UNP RESIDUES 263-383)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Gene: Tb927.7.2480 / Plasmid: PET41B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57XM6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.93 Å3/Da / Density % sol: 36.42 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 23 % PEG 4000, 100 MM NAACETATE / PH range: 7.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.970919 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.970919 Å / Relative weight: 1
ReflectionResolution: 1.35→18.5 Å / Num. obs: 22021 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 5.37 % / Biso Wilson estimate: 22.18 Å2 / Rmerge(I) obs: 0.021 / Net I/σ(I): 32.73
Reflection shellResolution: 1.35→1.39 Å / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 1.68 / % possible all: 67.5

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
MOLREPphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PIN1

Resolution: 1.35→18.46 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.75
RfactorNum. reflection% reflection
Rfree0.206 1101 5 %
Rwork0.166 --
obs0.168 22021 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.45 Å2
Refinement stepCycle: LAST / Resolution: 1.35→18.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 0 135 1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061005
X-RAY DIFFRACTIONf_angle_d1.1351368
X-RAY DIFFRACTIONf_dihedral_angle_d12.88394
X-RAY DIFFRACTIONf_chiral_restr0.069154
X-RAY DIFFRACTIONf_plane_restr0.004178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.41150.3311990.31681892X-RAY DIFFRACTION71
1.4115-1.48580.28531290.23512447X-RAY DIFFRACTION90
1.4858-1.57890.23931420.20362702X-RAY DIFFRACTION99
1.5789-1.70070.23421430.2042717X-RAY DIFFRACTION100
1.7007-1.87170.25291440.18692743X-RAY DIFFRACTION100
1.8717-2.14220.20881450.17112746X-RAY DIFFRACTION100
2.1422-2.69760.21951460.16842776X-RAY DIFFRACTION100
2.6976-18.46350.18071530.14692897X-RAY DIFFRACTION100
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)
14.6118-0.3191-0.55794.22780.51313.5074-0.0674-0.41090.02890.5722-0.07780.027-0.23-0.11780.10970.25970.0115-0.0290.24920.03190.1578.89797.4915-6.5966
28.3019-1.76325.44948.6139-0.85594.95840.0364-1.1381-0.55630.552-0.1276-0.17470.3113-0.02030.13720.21720.01890.05060.27250.06070.258517.2402-7.6586-14.7332
32.83290.3989-3.87835.50292.41197.0574-0.0999-0.4131-0.82980.3457-0.21540.64140.36890.04120.3180.15030.00780.03650.1962-0.0070.26094.5805-4.5884-18.5061
46.56483.56161.79318.2821-0.30651.40590.02020.0164-0.6828-0.0306-0.15520.48920.1395-0.10860.17710.17710.00440.02790.1669-0.00790.314213.697-8.1176-21.1562
53.2994-2.8199-1.46493.93841.6222.52440.07750.05660.2338-0.2238-0.0831-0.096-0.4503-0.0127-0.02080.2485-0.02-0.0250.19310.0160.220514.721911.3985-20.0733
62.27130.53260.9643.4164-0.24235.0795-0.0443-0.3145-0.08740.3942-0.1282-0.0113-0.2457-0.05560.14480.1578-0.0055-0.00340.17640.03580.14478.73115.914-8.8669
79.1719-4.9846-4.29797.73233.91362.6029-0.1468-0.10010.30870.3076-0.1749-0.2598-0.54570.25420.2360.3535-0.0476-0.07040.270.05630.229413.438915.8768-9.3914
84.90310.45862.06752.1312-0.10757.0715-0.1824-0.36880.00270.35110.1401-0.10790.02920.29560.13090.199-0.0099-0.03190.22260.05020.171814.00576.783-9.2199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 266 THROUGH 274 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 275 THROUGH 284 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 285 THROUGH 289 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 290 THROUGH 297 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 298 THROUGH 319 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 320 THROUGH 360 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 361 THROUGH 369 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 370 THROUGH 383 )

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