- PDB-3oan: Crystal structure of the Ran Binding Domain From The Nuclear Comp... -
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ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3oan
Title
Crystal structure of the Ran Binding Domain From The Nuclear Complex Component Nup2 From Ashbya Gossypii
Components
ABR034Wp
Keywords
TRANSPORT 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
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9791 Å / Relative weight: 1
Reflection
Resolution: 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
2.2-2.24
6.3
0.83
99.4
2.24-2.28
6.8
0.738
99.8
2.28-2.32
7.2
0.623
100
2.32-2.37
7.4
0.518
100
2.37-2.42
7.6
0.457
100
2.42-2.48
7.6
0.365
100
2.48-2.54
7.7
0.319
100
2.54-2.61
7.6
0.266
100
2.61-2.69
7.6
0.231
100
2.69-2.77
7.6
0.207
100
2.77-2.87
7.6
0.146
100
2.87-2.99
7.6
0.124
100
2.99-3.12
7.6
0.088
100
3.12-3.29
7.7
0.067
100
3.29-3.49
7.6
0.054
100
3.49-3.76
7.6
0.049
100
3.76-4.14
7.6
0.043
100
4.14-4.74
7.5
0.036
100
4.74-5.97
7.3
0.03
100
5.97-50
7.6
0.026
98.9
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
SCALEPACK
datascaling
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
CBASS
datacollection
HKL-2000
datareduction
PHENIX
phasing
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28869
354
4.7 %
RANDOM
Rwork
0.20934
-
-
-
obs
0.21302
7153
99.96 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 53.948 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.21 Å2
0 Å2
0 Å2
2-
-
0.21 Å2
0 Å2
3-
-
-
-0.42 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→19.98 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
916
0
6
37
959
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.022
940
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.213
1.99
1256
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.006
5
117
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.423
24.634
41
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.478
15
196
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.37
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
142
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
671
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.838
3.5
575
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
3.756
50
925
X-RAY DIFFRACTION
r_scbond_it
9.041
50
365
X-RAY DIFFRACTION
r_scangle_it
0.795
4.5
330
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.3→2.359 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.295
27
-
Rwork
0.265
516
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: 27.3961 Å / Origin y: 18.0178 Å / Origin z: 24.6684 Å
11
12
13
21
22
23
31
32
33
T
0.0282 Å2
0.0058 Å2
-0.0093 Å2
-
0.0329 Å2
-0.012 Å2
-
-
0.0189 Å2
L
3.7463 °2
0.054 °2
-0.3909 °2
-
4.1817 °2
1.166 °2
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-
3.1785 °2
S
0.0648 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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