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- PDB-3qtn: Structure of S. pombe nuclear import adaptor Nro1 (Space group P6522) -

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Basic information

Entry
Database: PDB / ID: 3qtn
TitleStructure of S. pombe nuclear import adaptor Nro1 (Space group P6522)
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 / MOLECULAR REPLACEMENT / Resolution: 3.499 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
Revision 1.3Nov 1, 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
B: Uncharacterized protein C4B3.07


Theoretical massNumber of molelcules
Total (without water)39,5061
Polymers39,5061
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.982, 123.982, 205.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein C4B3.07


Mass: 39505.984 Da / Num. of mol.: 1 / 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

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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: 5.7632 Å3/Da / Density % sol: 78.6576 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M Hepes pH 7.0, 1.6M ammonium sulphate, 10mM MgCl2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.499→25 Å / Num. all: 12281 / Num. obs: 11950 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 91.86 Å2 / Rsym value: 0.113 / Net I/σ(I): 11.3
Reflection shellResolution: 3.5→3.7 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QTM

3qtm


Resolution: 3.499→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8483 / SU ML: 0.32 / σ(F): 2 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 1232 10.01 %RANDOM
Rwork0.1951 ---
obs0.2003 11950 99.49 %-
all-13373 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.459 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 179.86 Å2 / Biso mean: 92.0555 Å2 / Biso min: 54.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.7706 Å2-0 Å20 Å2
2---0.7706 Å2-0 Å2
3---1.5411 Å2
Refinement stepCycle: LAST / Resolution: 3.499→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 0 0 2738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072794
X-RAY DIFFRACTIONf_angle_d0.9913806
X-RAY DIFFRACTIONf_chiral_restr0.068434
X-RAY DIFFRACTIONf_plane_restr0.003493
X-RAY DIFFRACTIONf_dihedral_angle_d20.86998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4994-3.63940.35511300.26061173130396
3.6394-3.80490.23531330.211611861319100
3.8049-4.00540.23051340.18812161350100
4.0054-4.25610.22211340.169812031337100
4.2561-4.58440.20531350.147212201355100
4.5844-5.0450.24631360.15312211357100
5.045-5.77350.25811380.179912431381100
5.7735-7.26790.21451410.197212651406100
7.2679-42.23740.22151510.16341351150299

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