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- PDB-4kf7: Nup188(aa1-1160) from Myceliophthora thermophila -

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Basic information

Entry
Database: PDB / ID: 4kf7
TitleNup188(aa1-1160) from Myceliophthora thermophila
ComponentsNup188
KeywordsSTRUCTURAL PROTEIN / Nucleoporin
Function / homology
Function and homology information


structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport
Similarity search - Function
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 / : / Nucleoporin Nup188, N-terminal subdomain III
Similarity search - Domain/homology
Biological speciesMyceliophthora thermophila (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 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
Revision 1.2Feb 28, 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: Nup188


Theoretical massNumber of molelcules
Total (without water)128,2461
Polymers128,2461
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.028, 94.773, 91.635
Angle α, β, γ (deg.)90.00, 98.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nup188


Mass: 128246.492 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-1160)
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 4.5-7.0% w/v PEG4000, 150 mM ammonium sulfate, 1 mM DTT, 1.0-2.5% tert-butanol, pH 6.5, 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: 2.65→66.8 Å / Num. all: 41673 / Num. obs: 41673 / % possible obs: 100 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 4.1 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 31.3
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
SHELXSphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.65→66.759 Å / SU ML: 0.34 / σ(F): 1.8 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 1919 4.61 %RANDOM
Rwork0.1807 ---
obs0.1829 41661 99.97 %-
all-41673 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→66.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8516 0 0 128 8644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048670
X-RAY DIFFRACTIONf_angle_d0.90411781
X-RAY DIFFRACTIONf_dihedral_angle_d13.8193164
X-RAY DIFFRACTIONf_chiral_restr0.0621388
X-RAY DIFFRACTIONf_plane_restr0.0041514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.71630.33421220.25052838X-RAY DIFFRACTION100
2.7163-2.78980.2831550.23222819X-RAY DIFFRACTION100
2.7898-2.87190.30421440.2292822X-RAY DIFFRACTION100
2.8719-2.96450.26781250.22432845X-RAY DIFFRACTION100
2.9645-3.07050.24131250.21592799X-RAY DIFFRACTION100
3.0705-3.19340.24871420.19372821X-RAY DIFFRACTION100
3.1934-3.33880.26111330.19282844X-RAY DIFFRACTION100
3.3388-3.51480.22231310.18052833X-RAY DIFFRACTION100
3.5148-3.7350.24621300.17422833X-RAY DIFFRACTION100
3.735-4.02330.21761350.16582841X-RAY DIFFRACTION100
4.0233-4.42810.20421290.15252854X-RAY DIFFRACTION100
4.4281-5.06870.19611510.15032843X-RAY DIFFRACTION100
5.0687-6.38520.23231450.20362847X-RAY DIFFRACTION100
6.3852-66.78010.18291520.16532903X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0256-0.37020.80411.6072-0.45330.6326-0.31750.9205-0.6267-0.32750.41690.17240.5006-0.0686-0.01780.5427-0.24250.06240.4969-0.26330.584640.050722.91635.3779
22.05630.37910.83771.9608-0.82881.3784-0.25490.83630.2767-0.10290.18021.0194-0.3915-0.3584-0.05450.5814-0.2669-0.10110.62520.0460.733522.847435.981433.1164
33.96072.17230.43381.441.15472.1548-0.36070.6115-0.191-0.20540.3050.01280.17260.01980.01330.3005-0.09510.02210.1581-0.01350.255346.940834.627142.3195
43.24091.2206-0.16271.88840.14152.8430.0053-0.15850.06120.0826-0.0054-0.10520.18170.2456-0.01730.18730.0473-0.0050.05150.01070.191662.400546.535760.004
53.27871.05291.91651.16391.04081.67090.2033-0.98780.12960.3222-0.44160.25770.3065-0.459-0.0440.4249-0.21230.13930.596-0.01270.354929.921632.534376.1061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 327 )
4X-RAY DIFFRACTION4chain 'A' and (resid 328 through 591 )
5X-RAY DIFFRACTION5chain 'A' and (resid 592 through 1149 )

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