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- PDB-1gy5: D92N,D94N double point mutant of human Nuclear Transport Factor 2... -

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Basic information

Entry
Database: PDB / ID: 1gy5
TitleD92N,D94N double point mutant of human Nuclear Transport Factor 2 (NTF2)
ComponentsNUCLEAR TRANSPORT FACTOR 2
KeywordsNUCLEAR TRANSPORT
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / 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 / nucleocytoplasmic transport / nuclear inner membrane / nuclear import signal receptor activity / mRNA transport ...small GTPase binding => GO:0031267 / 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 / nucleocytoplasmic transport / nuclear inner membrane / nuclear import signal receptor activity / 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 domain / Nuclear transport factor 2 (NTF2) 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 2.0May 22, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Refinement description
Category: atom_site / pdbx_database_proc ...atom_site / pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)28,9792
Polymers28,9792
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.040, 79.020, 42.140
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14489.456 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13662, UniProt: P61970*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.95 Å3/Da / Density % sol: 36.93 %
Crystal growpH: 4.5 / Details: pH 4.50
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 %PEG80001reservoir
2100 mMsodium acetate1reservoirpH4.5
350 mM1reservoirMgCl2
42.8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→18.1 Å / Num. obs: 7519 / % possible obs: 96.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.45
Reflection
*PLUS
Num. measured all: 18416
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.43 Å / % possible obs: 91.7 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 7.4

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→18 Å / Cross valid method: THROUGHOUT / Details: FIRST USED REFMAC, THEN CNS
RfactorNum. reflection% reflection
Rfree0.264 -5 %
Rwork0.222 --
obs-7519 96.6 %
Refinement stepCycle: LAST / Resolution: 2.3→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1980 0 0 65 2045
Refinement
*PLUS
Lowest resolution: 18 Å / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3

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