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- PDB-3rkv: C-terminal domain of protein C56C10.10, a putative peptidylprolyl... -

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Basic information

Entry
Database: PDB / ID: 3rkv
TitleC-terminal domain of protein C56C10.10, a putative peptidylprolyl isomerase, from Caenorhabditis elegans
Componentsputative peptidylprolyl isomerase
KeywordsISOMERASE / structural genomics / APC102156 / PSI-BIOLOGY / Midwest Center for Structural Genomics / MCSG / peptidylprolyl isomerase / TPR domain
Function / homology
Function and homology information


Aryl hydrocarbon receptor signalling / peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
: / AH receptor-interacting protein, N-terminal FKBP-type PPIase / AIP/AIPL1 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Peptidyl-prolyl cis-trans isomerase domain superfamily / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...: / AH receptor-interacting protein, N-terminal FKBP-type PPIase / AIP/AIPL1 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Peptidyl-prolyl cis-trans isomerase domain superfamily / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
TPR_REGION domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsOsipiuk, J. / Tesar, C. / Gu, M. / Van Oosten-Hawle, P. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: C-terminal domain of protein C56C10.10, a putative peptidylprolyl isomerase, from Caenorhabditis elegans
Authors: Osipiuk, J. / Tesar, C. / Gu, M. / Van Oosten-Hawle, P. / Morimoto, R.I. / Joachimiak, A.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative peptidylprolyl isomerase


Theoretical massNumber of molelcules
Total (without water)18,7961
Polymers18,7961
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.025, 84.674, 110.731
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein putative peptidylprolyl isomerase


Mass: 18796.326 Da / Num. of mol.: 1 / Fragment: C-terminal domain, residues 184-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: C56C10.10 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q18888
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 40% MPD, 0.1 M CHES , pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.41→42.4 Å / Num. all: 7946 / Num. obs: 7946 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 63.5 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.612 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.42-2.467.80.8151.983901.724100
2.46-2.518.20.8213861.653100
2.51-2.559.10.743801.531100
2.55-2.619.30.7073971.388100
2.61-2.669.60.6043891.406100
2.66-2.739.70.5473871.363100
2.73-2.799.70.4013891.442100
2.79-2.879.70.2993921.252100
2.87-2.959.70.2783881.252100
2.95-3.059.60.2134111.251100
3.05-3.169.70.1473841.212100
3.16-3.289.70.1223851.266100
3.28-3.439.70.1073941.425100
3.43-3.619.50.0834071.614100
3.61-3.849.50.074011.813100
3.84-4.149.50.0633912.125100
4.14-4.559.20.0584012.353100
4.55-5.219.20.0574122.178100
5.21-6.5690.0524101.675100
6.56-508.40.054522.395100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FBN

2fbn


Resolution: 2.41→42.3 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 26.662 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 366 4.6 %RANDOM
Rwork0.237 ---
all0.2401 7934 --
obs0.2401 7934 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 151.92 Å2 / Biso mean: 64.157 Å2 / Biso min: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.31 Å20 Å20 Å2
2--3.72 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.41→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1196 0 0 7 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221220
X-RAY DIFFRACTIONr_bond_other_d0.0030.02885
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9831640
X-RAY DIFFRACTIONr_angle_other_deg0.92932145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0575148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5523.65163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.615246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0151515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021338
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
X-RAY DIFFRACTIONr_mcbond_it0.7121.5738
X-RAY DIFFRACTIONr_mcbond_other0.1611.5293
X-RAY DIFFRACTIONr_mcangle_it1.33221183
X-RAY DIFFRACTIONr_scbond_it2.4313482
X-RAY DIFFRACTIONr_scangle_it4.164.5456
LS refinement shellResolution: 2.411→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 21 -
Rwork0.345 538 -
all-559 -
obs-559 96.38 %
Refinement TLS params.Method: refined / Origin x: 9.678 Å / Origin y: 32.3146 Å / Origin z: 26.2353 Å
111213212223313233
T0.1296 Å2-0.0333 Å20.0295 Å2-0.2972 Å20.0085 Å2--0.3339 Å2
L4.245 °2-0.4297 °2-0.4215 °2-3.482 °20.1703 °2--4.2185 °2
S-0.1051 Å °0.0979 Å °0.306 Å °-0.046 Å °0.2939 Å °-0.2156 Å °-0.1675 Å °0.3249 Å °-0.1887 Å °

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