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- PDB-4jde: Crystal structure of PUD-1/PUD-2 heterodimer -

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Basic information

Entry
Database: PDB / ID: 4jde
TitleCrystal structure of PUD-1/PUD-2 heterodimer
Components
  • Protein F15E11.1
  • Protein F15E11.13
KeywordsUNKNOWN FUNCTION / Beta sandwich
Function / homologyImmunoglobulin-like - #3820 / Up-regulated in Daf-2 / Up-Regulated in long-lived daf-2 / Immunoglobulin-like / Sandwich / Mainly Beta / Up-regulated in Daf-2 domain-containing protein / Up-regulated in Daf-2 domain-containing protein
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsLuo, S. / Ye, K.
CitationJournal: Plos One / Year: 2013
Title: Characterization of PUD-1 and PUD-2, two proteins up-regulated in a long-lived daf-2 mutant.
Authors: Ding, Y.H. / Du, Y.G. / Luo, S. / Li, Y.X. / Li, T.M. / Yoshina, S. / Wang, X. / Klage, K. / Mitani, S. / Ye, K. / Dong, M.Q.
History
DepositionFeb 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

Deposited unit
A: Protein F15E11.13
B: Protein F15E11.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,52513
Polymers33,0792
Non-polymers44711
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-93 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.991, 89.775, 102.503
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 Protein F15E11.13 / Protein Y19D10B.7


Mass: 16468.311 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 9-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F15E11.13, Y19D10B.7 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G5EET8
#2: Protein Protein F15E11.1 / Protein F15E11.14


Mass: 16610.477 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 7-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F15E11.1, F15E11.14 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G5EBF3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 3.69 Å3/Da / Density % sol: 66.62 % / Mosaicity: 0.55 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M HEPES (pH 7.2), 4.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99985 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 39660 / % possible obs: 98.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.073 / Χ2: 1.358 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.933.10.44617421.003188.6
1.93-1.973.50.38318970.925195.9
1.97-2.013.90.3619470.968198.9
2.01-2.054.20.32720020.984199.9
2.05-2.094.40.29219411.0731100
2.09-2.144.60.24419751.058199.8
2.14-2.194.60.21819791.048199.9
2.19-2.254.70.19519811.061100
2.25-2.324.70.17720011.1781100
2.32-2.394.70.14219571.0971100
2.39-2.484.70.12719911.128199.9
2.48-2.584.70.10920001.2331100
2.58-2.74.70.09319941.3291100
2.7-2.844.70.07520061.355199.9
2.84-3.014.70.06620001.5941100
3.01-3.254.60.06220192.097199.8
3.25-3.574.60.06820072.192199.5
3.57-4.094.60.06520392.3199.5
4.09-5.144.50.0420461.645199.3
5.14-254.40.03721361.386197.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.645 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 1964 5 %RANDOM
Rwork0.1917 ---
obs0.1934 38986 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.75 Å2 / Biso mean: 31.0333 Å2 / Biso min: 12.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 16 322 2653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022384
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.913226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03324.701117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81715415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.026159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021798
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 148 -
Rwork0.262 2357 -
all-2505 -
obs--93.68 %

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