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- PDB-2y8g: Structure of the Ran-binding domain from human RanBP3 (E352A-R353... -

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Basic information

Entry
Database: PDB / ID: 2y8g
TitleStructure of the Ran-binding domain from human RanBP3 (E352A-R353V double mutant)
ComponentsRAN-BINDING PROTEIN 3
KeywordsPROTEIN TRANSPORT / CRM1-MEDIATED NUCLEAR EXPORT
Function / homology
Function and homology information


R-SMAD binding / protein export from nucleus / small GTPase binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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
Ran-binding protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.61 Å
AuthorsLanger, K. / Dian, C. / Rybin, V. / Muller, C.W. / Petosa, C.
CitationJournal: Plos One / Year: 2011
Title: Insights Into the Function of the Crm1 Cofactor Ranbp3 from the Structure of its Ran-Binding Domain
Authors: Langer, K. / Dian, C. / Rybin, V. / Muller, C.W. / Petosa, C.
History
DepositionFeb 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: RAN-BINDING PROTEIN 3
B: RAN-BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1525
Polymers30,8632
Non-polymers2883
Water5,224290
1
A: RAN-BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6243
Polymers15,4321
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RAN-BINDING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5282
Polymers15,4321
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.320, 61.320, 137.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-2039-

HOH

21B-2091-

HOH

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Components

#1: Protein RAN-BINDING PROTEIN 3 / RANBP3-B


Mass: 15431.707 Da / Num. of mol.: 2 / Fragment: RAN BINDING DOMAIN, RESIDUES 320-454 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ISOFORM3 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6Z4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 352 TO ALA ENGINEERED RESIDUE IN CHAIN A, ARG 353 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, GLU 352 TO ALA ENGINEERED RESIDUE IN CHAIN A, ARG 353 TO VAL ENGINEERED RESIDUE IN CHAIN B, GLU 352 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 353 TO VAL
Sequence detailsGAM REMAINING RESIDUES FROM TEV CLEAVAGE SITE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.13 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.5 M LI2SO4, 100 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Details: BENT CYLINDRICAL MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.61→35 Å / Num. obs: 37445 / % possible obs: 94.7 % / Observed criterion σ(I): 3 / Redundancy: 10.7 % / Biso Wilson estimate: 17.69 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.7
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.3 / % possible all: 81.1

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHELXEphasing
PHENIXrefinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.61→34.654 Å / SU ML: 0.53 / σ(F): 1.37 / Phase error: 16.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1988 1862 5 %
Rwork0.1463 --
obs0.149 37433 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.485 Å2 / ksol: 0.416 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.3625 Å20 Å20 Å2
2---0.3625 Å20 Å2
3---0.7249 Å2
Refinement stepCycle: LAST / Resolution: 1.61→34.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 15 290 2169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041892
X-RAY DIFFRACTIONf_angle_d0.8452540
X-RAY DIFFRACTIONf_dihedral_angle_d13.526704
X-RAY DIFFRACTIONf_chiral_restr0.062299
X-RAY DIFFRACTIONf_plane_restr0.003317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6105-1.6540.23151110.17022001X-RAY DIFFRACTION70
1.654-1.70270.21581140.1292673X-RAY DIFFRACTION93
1.7027-1.75760.17581380.10732701X-RAY DIFFRACTION95
1.7576-1.82040.18051430.10172716X-RAY DIFFRACTION96
1.8204-1.89330.16011460.10012739X-RAY DIFFRACTION96
1.8933-1.97950.15261490.0982799X-RAY DIFFRACTION96
1.9795-2.08380.17461390.09492745X-RAY DIFFRACTION97
2.0838-2.21440.17731540.10492789X-RAY DIFFRACTION97
2.2144-2.38530.15781660.11052786X-RAY DIFFRACTION97
2.3853-2.62530.19261370.12862814X-RAY DIFFRACTION98
2.6253-3.0050.19491460.1422869X-RAY DIFFRACTION98
3.005-3.78520.18491490.15152891X-RAY DIFFRACTION98
3.7852-34.66190.24261700.19913048X-RAY DIFFRACTION99

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