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- PDB-4kf8: Nup188(aa1445-1827) from Myceliophthora thermophila -

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Basic information

Entry
Database: PDB / ID: 4kf8
TitleNup188(aa1445-1827) from Myceliophthora thermophila
ComponentsNup188Nucleoporin 188
KeywordsSTRUCTURAL PROTEIN / Nucleoporin
Function / homology
Function and homology information


structural constituent of nuclear pore / nuclear pore / protein transport
Similarity search - Function
Leucine-rich Repeat Variant - #70 / Nup188 SH3-like domain / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup188 / Leucine-rich Repeat Variant ...Leucine-rich Repeat Variant - #70 / Nup188 SH3-like domain / Nuclear pore protein Nup188, C-terminal / Nuclear pore protein NUP188 C-terminal domain / Nucleoporin Nup188, N-terminal / Nucleoporin Nup188, N-terminal / : / Nucleoporin Nup188, N-terminal subdomain III / Nucleoporin Nup188 / Leucine-rich Repeat Variant / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsSchwartz, T.U. / Andersen, K.R.
CitationJournal: Elife / Year: 2013
Title: Scaffold nucleoporins Nup188 and Nup192 share structural and functional properties with nuclear transport receptors.
Authors: Andersen, K.R. / Onischenko, E. / Tang, J.H. / Kumar, P. / Chen, J.Z. / Ulrich, A. / Liphardt, J.T. / Weis, K. / Schwartz, T.U.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nup188
B: Nup188


Theoretical massNumber of molelcules
Total (without water)82,8562
Polymers82,8562
Non-polymers00
Water0
1
A: Nup188


Theoretical massNumber of molelcules
Total (without water)41,4281
Polymers41,4281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nup188


Theoretical massNumber of molelcules
Total (without water)41,4281
Polymers41,4281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.298, 66.651, 162.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nup188 / Nucleoporin 188


Mass: 41428.156 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 1445-1827)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila (fungus) / Gene: MYCTH_2303581 / Production host: Escherichia coli (E. coli) / References: UniProt: G2QD05

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 18-23% w/v PEG3350, 150 mM tri-ammonium citrate, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→81.131 Å / Num. all: 14554 / Num. obs: 14539 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 21.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 4.8 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
SHELXSphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→81.131 Å / SU ML: 0.45 / σ(F): 4.8 / Phase error: 36.5 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2942 1137 7.82 %RANDOM
Rwork0.2753 ---
obs0.2769 14536 99.75 %-
all-14554 --
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→81.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 0 0 4366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034423
X-RAY DIFFRACTIONf_angle_d0.7696040
X-RAY DIFFRACTIONf_dihedral_angle_d13.4291519
X-RAY DIFFRACTIONf_chiral_restr0.05784
X-RAY DIFFRACTIONf_plane_restr0.004755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.13660.38511420.29231627X-RAY DIFFRACTION99
3.1366-3.3020.36761230.30341655X-RAY DIFFRACTION100
3.302-3.50880.37641390.27921652X-RAY DIFFRACTION100
3.5088-3.77980.33691310.29041662X-RAY DIFFRACTION100
3.7798-4.16010.33211450.26961656X-RAY DIFFRACTION100
4.1601-4.7620.27031460.2541673X-RAY DIFFRACTION100
4.762-5.99940.32371570.30081685X-RAY DIFFRACTION100
5.9994-81.16060.24011540.26421789X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.9167 Å / Origin y: 0.4767 Å / Origin z: -22.994 Å
111213212223313233
T0.5184 Å20.043 Å20.028 Å2-0.4045 Å20.0873 Å2--0.6971 Å2
L2.07 °20.3355 °21.2671 °2-2.0314 °21.8348 °2--4.7456 °2
S-0.2882 Å °0.177 Å °-0.1812 Å °0.044 Å °0.1075 Å °0.522 Å °0.2444 Å °0.4247 Å °-0.0144 Å °
Refinement TLS groupSelection details: all

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