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- PDB-5ji7: The Crystal Structure Of IUS-SPRY Domain From RanBPM/9 -

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Basic information

Entry
Database: PDB / ID: 5ji7
TitleThe Crystal Structure Of IUS-SPRY Domain From RanBPM/9
ComponentsRan-binding protein 9
KeywordsRAN-BINDING PROTEIN / BETA SANDWICH
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 / MAD / Resolution: 1.51 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / 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
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.697, 62.666, 69.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 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.: 221 / 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: 1.77 Å3/Da / Density % sol: 30.56 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 5C (4A)11
SYNCHROTRONPAL/PLS 5C (4A)20.97928, 0.97951, 0.97160
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 10, 2009
ADSC QUANTUM 2102CCDDec 10, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2MIRRORSMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979281
30.979511
40.97161
ReflectionResolution: 1.51→50 Å / Num. obs: 30090 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 44.825
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 10.683 / % possible all: 93.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: MAD / Resolution: 1.51→36.42 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.53 / Phase error: 14.97
RfactorNum. reflection% reflection
Rfree0.191 2000 6.71 %
Rwork0.163 --
obs0.165 29801 99.8 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 35.2 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.5774 Å2-0 Å2-0 Å2
2---0.0785 Å2-0 Å2
3----0.499 Å2
Refinement stepCycle: LAST / Resolution: 1.51→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 0 221 1780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071608
X-RAY DIFFRACTIONf_angle_d1.2512186
X-RAY DIFFRACTIONf_dihedral_angle_d13.875581
X-RAY DIFFRACTIONf_chiral_restr0.089222
X-RAY DIFFRACTIONf_plane_restr0.005289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5132-1.55110.20371370.17691904X-RAY DIFFRACTION99
1.5511-1.5930.19261410.15971954X-RAY DIFFRACTION100
1.593-1.63990.18861410.15891971X-RAY DIFFRACTION100
1.6399-1.69280.17881400.14851950X-RAY DIFFRACTION100
1.6928-1.75330.17551410.14641953X-RAY DIFFRACTION100
1.7533-1.82350.17921410.14191965X-RAY DIFFRACTION100
1.8235-1.90650.17051430.14421982X-RAY DIFFRACTION100
1.9065-2.0070.19351430.15481986X-RAY DIFFRACTION100
2.007-2.13270.20411420.15871971X-RAY DIFFRACTION100
2.1327-2.29740.17331430.16251993X-RAY DIFFRACTION100
2.2974-2.52850.21181440.16592006X-RAY DIFFRACTION100
2.5285-2.89430.1881450.17572004X-RAY DIFFRACTION100
2.8943-3.64590.19141460.17062044X-RAY DIFFRACTION100
3.6459-36.42860.19581530.17252118X-RAY DIFFRACTION99

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