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- PDB-1jb5: CRYSTAL STRUCTURE OF NTF2 M118E MUTANT -

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Basic information

Entry
Database: PDB / ID: 1jb5
TitleCRYSTAL STRUCTURE OF NTF2 M118E MUTANT
ComponentsNUCLEAR TRANSPORT FACTOR 2
KeywordsPROTEIN TRANSPORT / NTF2 / Transport
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChaillan-Huntington, C. / Butler, P.J. / Huntington, J.A. / Akin, D. / Feldherr, C. / Stewart, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: NTF2 monomer-dimer equilibrium.
Authors: Chaillan-Huntington, C. / Butler, P.J. / Huntington, J.A. / Akin, D. / Feldherr, C. / Stewart, M.
History
DepositionJun 1, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)28,9512
Polymers28,9512
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-16 kcal/mol
Surface area11480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.680, 78.210, 41.430
Angle α, β, γ (deg.)90.00, 104.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NUCLEAR TRANSPORT FACTOR 2


Mass: 14475.319 Da / Num. of mol.: 2 / Mutation: M118E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P61972
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.88 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.5 mg/mlprotein1drop
2100 mMsodium acetate1reservoirpH4.5
350 mM1reservoirMgCl2
426 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 9197 / Num. obs: 9197 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.272 / % possible all: 96.2
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. measured all: 73003
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 96.2 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JB4

1jb4


Resolution: 2.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Ergh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 475 5 %RANDOM
Rwork0.203 ---
all0.203 9197 --
obs0.203 9197 96.2 %-
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 0 112 2100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.5
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.3

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