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- PDB-1oun: CRYSTAL STRUCTURE OF NUCLEAR TRANSPORT FACTOR 2 (NTF2) -

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Basic information

Entry
Database: PDB / ID: 1oun
TitleCRYSTAL STRUCTURE OF NUCLEAR TRANSPORT FACTOR 2 (NTF2)
ComponentsNUCLEAR TRANSPORT FACTOR 2
KeywordsTRANSPORT / NUCLEAR TRANSPORT PROTEIN
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 / nuclear outer membrane / mRNA transport / protein export from nucleus / positive regulation of protein import into 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 / 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 / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SINGLE ISOMORPHOUS REPLACEMENT / Resolution: 2.3 Å
AuthorsBullock, T.L. / Stewart, M.J.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The 1.6 angstroms resolution crystal structure of nuclear transport factor 2 (NTF2).
Authors: Bullock, T.L. / Clarkson, W.D. / Kent, H.M. / Stewart, M.
#1: Journal: Structure / Year: 1994
Title: Crystal Structure of Scytalone Dehydratase--A Disease Determinant of the Rice Pathogen, Magnaporthe Grisea
Authors: Lundqvist, T. / Rice, J. / Hodge, C.N. / Basarab, G.S. / Pierce, J. / Lindqvist, Y.
History
DepositionFeb 21, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Other / Refinement description
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_database_status.process_site / _software.classification / _software.name
Revision 1.4Aug 14, 2019Group: Data collection / Category: computing
Revision 1.5Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-18 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.000, 58.100, 88.300
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 / PP15 / B2


Mass: 14491.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PET VECTOR / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P61972
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.48 Å3/Da / Density % sol: 47 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 5.5 / PH range high: 4.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %(w/v)PEG80001reservoir
225-100 mMmagnesium acetate1reservoir
3100 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 12825 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 4.1 / % possible all: 94.7
Reflection
*PLUS
Redundancy: 5.4 % / Num. measured all: 90240
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

Software
NameVersionClassification
TNTrefinement
SHELXrefinement
SHELXmodel building
MOSFLMdata reduction
CCP4(ROTAVATA)data scaling
SHELXphasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT
Resolution: 2.3→100 Å / σ(F): 0
Details: TNT LIBRARY RMS CO-ORDINATE SHIFT IN FINAL CYCLE (A) : 0.01
RfactorNum. reflection% reflection
Rfree0.23 -5 %
Rwork0.158 --
obs-12194 96.9 %
Refinement stepCycle: LAST / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 0 91 2071
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.010.02
X-RAY DIFFRACTIONt_angle_deg23
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.010.02
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_angle_deg2.1

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