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- PDB-1qma: Nuclear Transport Factor 2 (NTF2) W7A mutant -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1qma
TitleNuclear Transport Factor 2 (NTF2) W7A mutant
ComponentsNUCLEAR TRANSPORT FACTOR 2
KeywordsTRANSPORT
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 outer membrane / nuclear inner membrane / nuclear import signal receptor activity / nucleocytoplasmic transport / 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 outer membrane / nuclear inner membrane / nuclear import signal receptor activity / nucleocytoplasmic transport / mRNA transport / protein export from nucleus / small GTPase binding / positive regulation of protein import into nucleus / 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: 2.5 Å
AuthorsBayliss, R. / Ribbeck, K. / Akin, D. / Kent, H.M. / Feldherr, C.M. / Gorlich, D. / Stewart, M.J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Interaction Betweeen Ntf2 and Xfxfg-Containing Nucleoporins is Required to Mediate Nuclear Import of Ran-Gdp
Authors: Bayliss, R. / Ribbeck, K. / Akin, D. / Kent, H.M. / Feldherr, C.M. / Gorlich, D. / Stewart, M.J.
History
DepositionSep 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2000Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,9804
Polymers56,9804
Non-polymers00
Water1,51384
1
A: NUCLEAR TRANSPORT FACTOR 2
B: NUCLEAR TRANSPORT FACTOR 2


Theoretical massNumber of molelcules
Total (without water)28,4902
Polymers28,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-27.2 kcal/mol
Surface area15300 Å2
MethodPQS
2
C: NUCLEAR TRANSPORT FACTOR 2
D: NUCLEAR TRANSPORT FACTOR 2


Theoretical massNumber of molelcules
Total (without water)28,4902
Polymers28,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-25.4 kcal/mol
Surface area15050 Å2
MethodPQS
Unit cell
Length a, b, c (Å)64.652, 75.407, 64.543
Angle α, β, γ (deg.)90.00, 115.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.42188, 0.00021, -0.90665), (0.00023, -1, -0.00013), (-0.90665, -0.00015, -0.42188)18.64296, 34.0858, 29.27585
2given(0.42467, -0.00066, -0.90535), (-0.0006, -1, 0.00045), (-0.90535, 0.00036, -0.42467)18.56357, 34.08558, 29.30314
DetailsBIOLOGICAL_UNIT: DIMERIC

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Components

#1: Protein
NUCLEAR TRANSPORT FACTOR 2 / NTF2 / PLACENTAL PROTEIN 15 / PP15


Mass: 14245.100 Da / Num. of mol.: 4 / Mutation: YES
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): BL21(DE3) / References: UniProt: P13662, UniProt: P61972*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 mg/mlprotein1drop
21.32 Mammonium sulfate1reservoir
33 %(v/v)isopropanol1reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.5→22.7 Å / Num. obs: 18928 / % possible obs: 97.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 3.5 / % possible all: 91.8
Reflection
*PLUS
Num. measured all: 65817
Reflection shell
*PLUS
% possible obs: 91.8 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OUN

1oun


Resolution: 2.5→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.24 -5 %
Rwork0.208 --
obs-16569 100 %
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 0 84 4054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.033
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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