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- PDB-1ask: NUCLEAR TRANSPORT FACTOR 2 (NTF2) H66A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1ask
TitleNUCLEAR TRANSPORT FACTOR 2 (NTF2) H66A MUTANT
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMccoy, A.J. / Stewart, M.J.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Nuclear protein import is decreased by engineered mutants of nuclear transport factor 2 (NTF2) that do not bind GDP-Ran.
Authors: Clarkson, W.D. / Corbett, A.H. / Paschal, B.M. / Kent, H.M. / McCoy, A.J. / Gerace, L. / Silver, P.A. / Stewart, M.
#1: 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.
#2: 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
DepositionAug 11, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)28,8492
Polymers28,8492
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-19 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.000, 57.460, 87.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.904075, 0.132174, 0.406423), (0.129891, -0.82101, 0.555942), (0.407158, 0.555403, 0.725086)
Vector: 39.6257, 8.1867, -11.334)

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Components

#1: Protein NUCLEAR TRANSPORT FACTOR 2 / PP15 / B2


Mass: 14424.356 Da / Num. of mol.: 2 / Mutation: H66A
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.: 55 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion / Details: Kent, H.M., (1996) J. Struct. Biol., 116, 325.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
22.5 mMTris-HCl1drop
350 mMsodium acetate1drop
45 %PEG80001drop
51 mMsodium azide1drop
6100 mMsodium acetate1reservoir
710 %PEG80001reservoir
82 mMsodium azide1reservoir

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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: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 10657 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.7 / % possible all: 91.5

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Processing

Software
NameVersionClassification
CCP4model building
REFMACrefinement
MOSFLMdata reduction
CCP4(ROTAVATA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OUN (NTF2)

1oun


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: DIHEDRAL ANGLES FOR ASP 92 LIE OUTSIDE THE EXPECTED RANGE, BUT THE RESIDUE IS IN GOOD ELECTRON DENSITY AND THE DIHEDRAL ANGLES HAVE A SIMILAR CONFORMATION IN THE NATIVE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.24285 626 5 %RANDOM
Rwork0.19965 ---
obs-12533 96.2 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 55 2065
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 12533 / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_deg2.7

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