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- PDB-3n7c: Crystal structure of the RAN binding domain from the nuclear pore... -

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Basic information

Entry
Database: PDB / ID: 3n7c
TitleCrystal structure of the RAN binding domain from the nuclear pore complex component NUP2 from Ashbya gossypii
ComponentsABR034Wp
KeywordsPROTEIN TRANSPORT / Nuclear pore complex / NUP2 / Ran-binding domain / Nucleoporin / STRUCTURAL GENOMICS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / nuclear pore nuclear basket / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus ...mRNA export from nucleus in response to heat stress / protein localization to nuclear inner membrane / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / nuclear pore nuclear basket / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / structural constituent of nuclear pore / silent mating-type cassette heterochromatin formation / poly(A)+ mRNA export from nucleus / NLS-bearing protein import into nucleus / subtelomeric heterochromatin formation / nuclear pore / protein export from nucleus / small GTPase binding / chromosome, telomeric region / cytoplasm
Similarity search - Function
Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesAshbya gossypii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsSampathkumar, P. / Manglicmot, D. / Gilmore, J. / Bain, K. / Gheyi, T. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. ...Sampathkumar, P. / Manglicmot, D. / Gilmore, J. / Bain, K. / Gheyi, T. / Atwell, S. / Thompson, D.A. / Emtage, J.S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the RAN binding domain from the nuclear pore complex component NUP2 from Ashbya gossypii
Authors: Sampathkumar, P.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABR034Wp
B: ABR034Wp


Theoretical massNumber of molelcules
Total (without water)29,6412
Polymers29,6412
Non-polymers00
Water48627
1
A: ABR034Wp


Theoretical massNumber of molelcules
Total (without water)14,8211
Polymers14,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ABR034Wp


Theoretical massNumber of molelcules
Total (without water)14,8211
Polymers14,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.540, 62.550, 76.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ABR034Wp


Mass: 14820.566 Da / Num. of mol.: 2 / Fragment: sequence database residues 497-615
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (fungus) / Strain: ATCC 10895 / Gene: ABR034W, AGOS_ABR034W, NUP2 / Plasmid: BC-pSGX3(BC); modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: Q75DJ0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM Bis-Tris pH 5.5 + 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 10, 2010
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.26→38.12 Å / Num. obs: 13396 / % possible obs: 99.7 % / Redundancy: 13.5 % / Biso Wilson estimate: 42.54 Å2 / Rsym value: 0.103 / Net I/σ(I): 15.7
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 1925 / Rsym value: 0.58 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
SHELXCphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.26→21.17 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.248 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.241
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.293 654 4.9 %RANDOM
Rwork0.234 ---
obs0.236 13335 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 71.73 Å2 / Biso mean: 43.78 Å2 / Biso min: 23.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.26→21.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 0 27 1589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221619
X-RAY DIFFRACTIONr_bond_other_d0.0010.021086
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9772191
X-RAY DIFFRACTIONr_angle_other_deg0.98232658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6065215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84623.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85915283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6311512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02324
X-RAY DIFFRACTIONr_mcbond_it1.1631.51054
X-RAY DIFFRACTIONr_mcbond_other0.2391.5438
X-RAY DIFFRACTIONr_mcangle_it2.18821671
X-RAY DIFFRACTIONr_scbond_it2.9073565
X-RAY DIFFRACTIONr_scangle_it4.5994.5514
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 54 -
Rwork0.255 908 -
all-962 -
obs--100 %

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