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- PDB-1gyb: N77Y point mutant of yNTF2 bound to FxFG nucleoporin repeat -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1gyb
TitleN77Y point mutant of yNTF2 bound to FxFG nucleoporin repeat
Components
  • NUCLEAR TRANSPORT FACTOR 2
  • NUCLEOPORIN
KeywordsNUCLEAR TRANSPORT
Function / homology
Function and homology information


nuclear pore central transport channel / nuclear import signal receptor activity / nucleocytoplasmic transport / small GTPase binding / protein import into nucleus / nuclear envelope / cytoplasm
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 speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2002Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2May 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
C: NUCLEAR TRANSPORT FACTOR 2
D: NUCLEAR TRANSPORT FACTOR 2
E: NUCLEOPORIN
F: NUCLEOPORIN
G: NUCLEOPORIN
H: NUCLEOPORIN


Theoretical massNumber of molelcules
Total (without water)61,7768
Polymers61,7768
Non-polymers00
Water6,918384
1
A: NUCLEAR TRANSPORT FACTOR 2
B: NUCLEAR TRANSPORT FACTOR 2
E: NUCLEOPORIN
F: NUCLEOPORIN


Theoretical massNumber of molelcules
Total (without water)30,8884
Polymers30,8884
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: NUCLEAR TRANSPORT FACTOR 2
D: NUCLEAR TRANSPORT FACTOR 2
G: NUCLEOPORIN
H: NUCLEOPORIN


Theoretical massNumber of molelcules
Total (without water)30,8884
Polymers30,8884
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.840, 84.060, 61.790
Angle α, β, γ (deg.)90.00, 116.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NUCLEAR TRANSPORT FACTOR 2 / NTF-2 / NUCLEAR TRANSPORT FACTOR P10


Mass: 14512.100 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P33331
#2: Protein/peptide
NUCLEOPORIN


Mass: 931.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growpH: 6.5
Details: 100MM AMMONIUM ACETATE PH 6.5, 1.6M AMMONIUM SULPHATE
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMammonium acetate1droppH6.5
20.8 Mammonium sulfate1drop
33.5 mg/mlprotein1drop
46.25 MFF11drop
5100 mMammonium acetate1reservoirpH6.5
61.52 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→53 Å / Num. obs: 39224 / % possible obs: 92.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.7 / % possible all: 88.3
Reflection
*PLUS
Lowest resolution: 53 Å / Num. measured all: 266201 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 88.3 %

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Processing

Software
NameClassification
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 -5 %SAME AS XXX
Rwork0.197 ---
obs0.197 39224 92.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 0 384 4475
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.42
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: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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