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- PDB-5ji9: The Crystal Structure Of IUS-SPRY Domain From RanBPM/9 -

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Basic information

Entry
Database: PDB / ID: 5ji9
TitleThe Crystal Structure Of IUS-SPRY Domain From RanBPM/9
ComponentsRan-binding protein 9
KeywordsRAN-BINDING PROTEIN / BETA SANDWICH / TRANSPORT PROTEIN
Function / homology
Function and homology information


L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / microtubule nucleation / microtubule associated complex / MET activates RAS signaling / ubiquitin ligase complex / cytoskeleton organization / negative regulation of ERK1 and ERK2 cascade / small GTPase binding / RAF/MAP kinase cascade ...L1CAM interactions / positive regulation of amyloid precursor protein catabolic process / microtubule nucleation / microtubule associated complex / MET activates RAS signaling / ubiquitin ligase complex / cytoskeleton organization / negative regulation of ERK1 and ERK2 cascade / small GTPase binding / RAF/MAP kinase cascade / protein-containing complex assembly / nuclear body / enzyme binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ran binding protein 9/10, SPRY domain / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / LisH / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / SPRY domain ...Ran binding protein 9/10, SPRY domain / CRA domain / CT11-RanBPM / CTLH/CRA C-terminal to LisH motif domain / CTLH/CRA C-terminal to LisH motif domain / LisH / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / SPRY domain / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ran-binding protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHong, S.K. / Kim, K.-H. / Kim, E.E.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Ministry of ScienceNRF 20110021713 Korea, Republic Of
Korea Institute of Science and Technology Korea, Republic Of
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development.
Authors: Hong, S.K. / Kim, K.H. / Song, E.J. / Kim, E.E.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ran-binding protein 9


Theoretical massNumber of molelcules
Total (without water)26,3441
Polymers26,3441
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.478, 69.478, 107.688
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Ran-binding protein 9 / RanBP9 / BPM-L / BPM90 / Ran-binding protein M / RanBPM / RanBP7


Mass: 26344.484 Da / Num. of mol.: 1 / Fragment: IUS-SPRY DOMAIN, UNP RESIDUES 108-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RANBP9, RANBPM / Plasmid: MODIFIED PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: Q96S59
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.85 Å3/Da / Density % sol: 62.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M NA-CACODYLATE, PH 6.5, 6% PEG 4000, 0.2M KCL, 0.02M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2009
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10287 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Net I/σ(I): 22.0625
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.284 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JI7

5ji7


Resolution: 2.5→40.12 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.5 / Phase error: 21.05
RfactorNum. reflection% reflection
Rfree0.227 1024 10.05 %
Rwork0.167 --
obs0.173 10194 99.5 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 37.47 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5448 Å20 Å2-0 Å2
2--3.5448 Å2-0 Å2
3----7.0896 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 55 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081662
X-RAY DIFFRACTIONf_angle_d1.1682258
X-RAY DIFFRACTIONf_dihedral_angle_d15.684606
X-RAY DIFFRACTIONf_chiral_restr0.076228
X-RAY DIFFRACTIONf_plane_restr0.005301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5005-2.63230.32321420.24611285X-RAY DIFFRACTION97
2.6323-2.79720.27361470.21521317X-RAY DIFFRACTION100
2.7972-3.01310.23821430.18751302X-RAY DIFFRACTION100
3.0131-3.31620.24221410.1651314X-RAY DIFFRACTION100
3.3162-3.79580.23841470.151311X-RAY DIFFRACTION100
3.7958-4.7810.1981460.13331309X-RAY DIFFRACTION100
4.781-40.12930.19021580.16591332X-RAY DIFFRACTION100

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