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- PDB-3qtm: Structure of S. pombe nuclear import adaptor Nro1 (Space group P21) -

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Basic information

Entry
Database: PDB / ID: 3qtm
TitleStructure of S. pombe nuclear import adaptor Nro1 (Space group P21)
ComponentsUncharacterized protein C4B3.07
KeywordsTRANSLATION / Tetratricopeptide repeat / Enhancer of translation termination
Function / homology
Function and homology information


positive regulation of SREBP signaling pathway / cation binding / SREBP signaling pathway / regulation of translation / cellular response to hypoxia / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Negative regulator of Ofd1/Enhancer of translation termination 1 / Nuclear pore complex subunit Nro1
Similarity search - Domain/homology
Negative regulator of ofd1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsRispal, D. / Henri, J. / van Tilbeurgh, H. / Graille, M. / Seraphin, B.
CitationJournal: Rna / Year: 2011
Title: Structural and functional analysis of Nro1/Ett1: a protein involved in translation termination in S. cerevisiae and in O2-mediated gene control in S. pombe
Authors: Rispal, D. / Henri, J. / van Tilbeurgh, H. / Graille, M. / Seraphin, B.
History
DepositionFeb 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Structure summary
Revision 1.2Jan 3, 2018Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein C4B3.07
B: Uncharacterized protein C4B3.07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0829
Polymers79,6332
Non-polymers4497
Water10,215567
1
A: Uncharacterized protein C4B3.07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0104
Polymers39,8171
Non-polymers1943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein C4B3.07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0725
Polymers39,8171
Non-polymers2564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.930, 107.840, 101.790
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein C4B3.07


Mass: 39816.574 Da / Num. of mol.: 2 / Fragment: UNP residues 56-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPCC4B3.07 / Plasmid: pET21-a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q9USJ7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 3.3 Å3/Da / Density % sol: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Hepes pH 7.0, 1.6M ammonium sulphate, 10mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791, 0.97946, 0.95373
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.979461
30.953731
ReflectionResolution: 2.15→40 Å / Num. obs: 55704 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rsym value: 0.089 / Net I/σ(I): 6.3
Reflection shellResolution: 2.15→2.3 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.467 / % possible all: 86.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.15→39.9 Å / SU ML: 0.28 / σ(F): 1.39 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 2827 5.08 %RANDOM
Rwork0.1779 ---
all0.1797 56083 --
obs0.1797 55668 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.117 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.0667 Å2-0 Å2-0.3967 Å2
2---1.8982 Å2-0 Å2
3---1.965 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 0 24 567 5876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075424
X-RAY DIFFRACTIONf_angle_d0.917383
X-RAY DIFFRACTIONf_dihedral_angle_d17.9491955
X-RAY DIFFRACTIONf_chiral_restr0.059840
X-RAY DIFFRACTIONf_plane_restr0.008955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.18720.28031150.22952265X-RAY DIFFRACTION86
2.1872-2.22690.28331420.21492677X-RAY DIFFRACTION100
2.2269-2.26980.25171520.21182605X-RAY DIFFRACTION100
2.2698-2.31610.26761430.19672688X-RAY DIFFRACTION100
2.3161-2.36640.22791340.18412648X-RAY DIFFRACTION100
2.3664-2.42150.25831310.18572651X-RAY DIFFRACTION100
2.4215-2.4820.22751480.18562651X-RAY DIFFRACTION100
2.482-2.54910.2281470.18272661X-RAY DIFFRACTION100
2.5491-2.62410.25371300.18572655X-RAY DIFFRACTION100
2.6241-2.70880.2371260.18612696X-RAY DIFFRACTION100
2.7088-2.80560.24841310.19052646X-RAY DIFFRACTION100
2.8056-2.91790.21021590.18962652X-RAY DIFFRACTION100
2.9179-3.05070.25661330.18832681X-RAY DIFFRACTION100
3.0507-3.21140.21821630.18422615X-RAY DIFFRACTION100
3.2114-3.41250.19821490.17152644X-RAY DIFFRACTION100
3.4125-3.67580.18611700.15142646X-RAY DIFFRACTION100
3.6758-4.04540.18191330.14892698X-RAY DIFFRACTION100
4.0454-4.63010.18421470.1462648X-RAY DIFFRACTION100
4.6301-5.83050.18441500.17362687X-RAY DIFFRACTION100
5.8305-39.90690.17991240.17652727X-RAY DIFFRACTION99

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