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- PDB-3oan: Crystal structure of the Ran Binding Domain From The Nuclear Comp... -

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Basic information

Entry
Database: PDB / ID: 3oan
TitleCrystal structure of the Ran Binding Domain From The Nuclear Complex Component Nup2 From Ashbya Gossypii
ComponentsABR034Wp
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / PSI-2 / 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 / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / 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 / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / 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: 2.3 Å
AuthorsMalashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the Ran Binding Domain From The Nuclear Complex Component Nup2 From Ashbya Gossypii
Authors: Malashkevich, V.N. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABR034Wp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9882
Polymers14,8961
Non-polymers921
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.691, 65.691, 72.869
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ABR034Wp


Mass: 14895.514 Da / Num. of mol.: 1 / Fragment: C-terminal residues 497-615 / Mutation: C54M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ashbya gossypii (fungus) / Strain: TCC 10895 / Gene: ABR034W, AGOS_ABR034W / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q75DJ0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG8000, 0.1M na-cacodylate, 0.2 M sodium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 15579 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.2-2.246.30.8399.4
2.24-2.286.80.73899.8
2.28-2.327.20.623100
2.32-2.377.40.518100
2.37-2.427.60.457100
2.42-2.487.60.365100
2.48-2.547.70.319100
2.54-2.617.60.266100
2.61-2.697.60.231100
2.69-2.777.60.207100
2.77-2.877.60.146100
2.87-2.997.60.124100
2.99-3.127.60.088100
3.12-3.297.70.067100
3.29-3.497.60.054100
3.49-3.767.60.049100
3.76-4.147.60.043100
4.14-4.747.50.036100
4.74-5.977.30.03100
5.97-507.60.02698.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.98 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.354 / SU ML: 0.171 / SU R Cruickshank DPI: 0.2704 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28869 354 4.7 %RANDOM
Rwork0.20934 ---
obs0.21302 7153 99.96 %-
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 mean: 53.948 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 6 37 959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2131.991256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0065117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.42324.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47815196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.37157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02671
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8383.5575
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.75650925
X-RAY DIFFRACTIONr_scbond_it9.04150365
X-RAY DIFFRACTIONr_scangle_it0.7954.5330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 27 -
Rwork0.265 516 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 27.3961 Å / Origin y: 18.0178 Å / Origin z: 24.6684 Å
111213212223313233
T0.0282 Å20.0058 Å2-0.0093 Å2-0.0329 Å2-0.012 Å2--0.0189 Å2
L3.7463 °20.054 °2-0.3909 °2-4.1817 °21.166 °2--3.1785 °2
S0.0648 Å °0.2792 Å °-0.1241 Å °-0.1679 Å °-0.1537 Å °0.1921 Å °-0.1845 Å °-0.0535 Å °0.089 Å °

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