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- PDB-5jia: The Crystal Structure Of IUS-SPRY Domain From RanBP10 -

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Basic information

Entry
Database: PDB / ID: 5jia
TitleThe Crystal Structure Of IUS-SPRY Domain From RanBP10
ComponentsRan-binding protein 10
KeywordsRAN-BINDING PROTEIN / BETA SANDWICH / TRANSPORT PROTEIN
Function / homology
Function and homology information


MET activates RAS signaling / ubiquitin ligase complex / beta-tubulin binding / cytoskeleton organization / guanyl-nucleotide exchange factor activity / small GTPase binding / microtubule cytoskeleton organization / microtubule cytoskeleton / nucleus / 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. ...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 / LIS1 homology (LisH) motif profile. / LIS1 homology motif / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / Ran-binding protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 10
B: Ran-binding protein 10
C: Ran-binding protein 10
D: Ran-binding protein 10
E: Ran-binding protein 10
F: Ran-binding protein 10
G: Ran-binding protein 10
H: Ran-binding protein 10
I: Ran-binding protein 10
J: Ran-binding protein 10
K: Ran-binding protein 10
L: Ran-binding protein 10
M: Ran-binding protein 10
N: Ran-binding protein 10
O: Ran-binding protein 10
P: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,92124
Polymers372,36916
Non-polymers5538
Water41,8132321
1
A: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3422
Polymers23,2731
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)23,2731
Polymers23,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)23,2731
Polymers23,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3422
Polymers23,2731
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3422
Polymers23,2731
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)23,2731
Polymers23,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3422
Polymers23,2731
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3422
Polymers23,2731
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)23,2731
Polymers23,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3422
Polymers23,2731
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)23,2731
Polymers23,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)23,2731
Polymers23,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)23,2731
Polymers23,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3422
Polymers23,2731
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Ran-binding protein 10


Theoretical massNumber of molelcules
Total (without water)23,2731
Polymers23,2731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Ran-binding protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3422
Polymers23,2731
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.340, 79.240, 157.630
Angle α, β, γ (deg.)90.00, 97.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ran-binding protein 10 / RanBP10


Mass: 23273.049 Da / Num. of mol.: 16 / Fragment: IUS-SPRY DOMAIN, UNP RESIDUES 29-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ranbp10, Kiaa1464 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: Q6VN19
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2321 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M BICINE, PH 9.0, 10% PEG 20000, 0- 2% DIOXANE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
PH range: 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 20, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 330519 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 14.159
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.563 / % possible all: 85.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JI7

5ji7


Resolution: 1.8→41.25 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.49 / Phase error: 21.04
RfactorNum. reflection% reflection
Rfree0.227 1988 65 %
Rwork0.184 306107 -
obs0.184 306107 92.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→41.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25622 0 40 2321 27983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726454
X-RAY DIFFRACTIONf_angle_d1.19435885
X-RAY DIFFRACTIONf_dihedral_angle_d13.9869543
X-RAY DIFFRACTIONf_chiral_restr0.0833598
X-RAY DIFFRACTIONf_plane_restr0.0074773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84520.28491360.246819737X-RAY DIFFRACTION85
1.8452-1.8950.28951460.229820132X-RAY DIFFRACTION86
1.895-1.95080.22371190.213820661X-RAY DIFFRACTION89
1.9508-2.01380.24561350.195520922X-RAY DIFFRACTION90
2.0138-2.08570.26261450.195121240X-RAY DIFFRACTION91
2.0857-2.16920.23161370.190921332X-RAY DIFFRACTION91
2.1692-2.2680.24491400.183921732X-RAY DIFFRACTION93
2.268-2.38750.2461460.184821724X-RAY DIFFRACTION93
2.3875-2.53710.22821410.184922155X-RAY DIFFRACTION95
2.5371-2.73290.2411460.187422411X-RAY DIFFRACTION95
2.7329-3.00790.24021520.184422565X-RAY DIFFRACTION96
3.0079-3.4430.2231410.182822819X-RAY DIFFRACTION97
3.443-4.3370.1921490.159422966X-RAY DIFFRACTION97
4.337-41.26320.1921550.166123723X-RAY DIFFRACTION99

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