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- PDB-1gy6: NTF2 from rat, ammonium sulphate conditions -

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Basic information

Entry
Database: PDB / ID: 1gy6
TitleNTF2 from rat, ammonium sulphate conditions
ComponentsNUCLEAR TRANSPORT FACTOR 2
KeywordsNUCLEAR TRANSPORT
Function / homology
Function and homology information


negative regulation of vascular endothelial growth factor production / protein localization to nuclear pore / nuclear pore central transport channel / structural constituent of nuclear pore / nuclear inner membrane / nuclear import signal receptor activity / nucleocytoplasmic transport / nuclear outer membrane / mRNA transport / protein export from nucleus ...negative regulation of vascular endothelial growth factor production / protein localization to nuclear pore / nuclear pore central transport channel / structural constituent of nuclear pore / nuclear inner membrane / nuclear import signal receptor activity / nucleocytoplasmic transport / nuclear outer membrane / mRNA transport / protein export from nucleus / positive regulation of protein import into nucleus / small GTPase binding / protein import into nucleus / nuclear membrane / extracellular exosome / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Nuclear transport factor 2/Mtr2 / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Nuclear transport factor 2 / Nuclear transport factor 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBayliss, R. / Stewart, M.
CitationJournal: Embo J. / Year: 2002
Title: Structural Basis for the Interaction between Ntf2 and Nucleoporin Fxfg Repeats
Authors: Bayliss, R. / Leung, S. / Baker, R. / Quimby, B. / Corbett, A. / Stewart, M.
History
DepositionApr 21, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEAR TRANSPORT FACTOR 2
B: NUCLEAR TRANSPORT FACTOR 2


Theoretical massNumber of molelcules
Total (without water)28,9832
Polymers28,9832
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.540, 57.390, 86.890
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 NUCLEAR TRANSPORT FACTOR 2 / NTF-2 / PLACENTAL PROTEIN 15 / PP15


Mass: 14491.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13662, UniProt: P61972*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growpH: 5.5
Details: 100MM AMMONIUM ACETATE PH 5.5, 1.2M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.6→36.3 Å / Num. obs: 36958 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 24.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.6 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 234160
Reflection shell
*PLUS
% possible obs: 93.5 % / Rmerge(I) obs: 0.19

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OUN

1oun


Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 -5 %RANDOM
Rwork0.212 ---
obs0.212 36958 98.6 %-
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 181 2177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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