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- PDB-4r3f: Structure of the spliceosomal peptidyl-prolyl cis-trans isomerase... -

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Basic information

Entry
Database: PDB / ID: 4r3f
TitleStructure of the spliceosomal peptidyl-prolyl cis-trans isomerase Cwc27 from Chaetomium thermophilum
Componentsspliceosomal protein CWC27Spliceosome
KeywordsISOMERASE / Cyclophilin-type PPIase / nucleus
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity / protein folding
Similarity search - Function
Cyclophilin-like / Cyclophilin / 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
ACETATE ION / PPIase cyclophilin-type domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsUlrich, A. / Wahl, M.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure and evolution of the spliceosomal peptidyl-prolyl cis-trans isomerase Cwc27.
Authors: Ulrich, A. / Wahl, M.C.
History
DepositionAug 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: spliceosomal protein CWC27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,41612
Polymers22,4001
Non-polymers1,01611
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.613, 58.652, 59.305
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 spliceosomal protein CWC27 / Spliceosome


Mass: 22400.055 Da / Num. of mol.: 1 / Fragment: PPIase domain, UNP residues 2-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0005290 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: G0RY38, peptidylprolyl isomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate (pH 4.6) 8% PEG 4,000, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 10, 2013
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→33.98 Å / Num. obs: 49755 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 16.9 % / Biso Wilson estimate: 19.1 Å2 / Net I/σ(I): 29.7
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 3368 / % possible all: 90.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HQ6

2hq6


Resolution: 1.3→33.979 Å / SU ML: 0.07 / σ(F): 1.36 / Phase error: 11.93 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.143 2522 5.07 %RANDOM
Rwork0.1209 ---
obs0.122 49755 97.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 50 265 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081710
X-RAY DIFFRACTIONf_angle_d1.2462305
X-RAY DIFFRACTIONf_dihedral_angle_d14.919643
X-RAY DIFFRACTIONf_chiral_restr0.078229
X-RAY DIFFRACTIONf_plane_restr0.007318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3001-1.32510.18911050.13632373X-RAY DIFFRACTION89
1.3251-1.35210.16091400.12522524X-RAY DIFFRACTION96
1.3521-1.38150.15511420.11562550X-RAY DIFFRACTION96
1.3815-1.41370.15151420.11412526X-RAY DIFFRACTION96
1.4137-1.4490.16091570.10932509X-RAY DIFFRACTION97
1.449-1.48820.1451420.10542610X-RAY DIFFRACTION97
1.4882-1.5320.13831390.10192590X-RAY DIFFRACTION98
1.532-1.58150.12071380.10162633X-RAY DIFFRACTION98
1.5815-1.6380.11721390.09982633X-RAY DIFFRACTION98
1.638-1.70360.12741390.10262631X-RAY DIFFRACTION99
1.7036-1.78110.15121360.10482618X-RAY DIFFRACTION98
1.7811-1.8750.12881400.10282659X-RAY DIFFRACTION99
1.875-1.99240.12061410.10832662X-RAY DIFFRACTION99
1.9924-2.14630.12921400.10372671X-RAY DIFFRACTION99
2.1463-2.36220.11941420.10962701X-RAY DIFFRACTION99
2.3622-2.70390.1131430.11762709X-RAY DIFFRACTION100
2.7039-3.40610.16171450.13042751X-RAY DIFFRACTION100
3.4061-33.9910.1721520.15152883X-RAY DIFFRACTION100

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