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- PDB-6bk4: Crystal structure of the HR-1 domain of Drosophila caprin in the ... -

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Basic information

Entry
Database: PDB / ID: 6bk4
TitleCrystal structure of the HR-1 domain of Drosophila caprin in the P212121 space group
ComponentsCaprin homolog
KeywordsRNA BINDING PROTEIN / RNA-Binding / Alpha-helical / FMRP parnter / cellular proliferation
Function / homology
Function and homology information


regulation of mitotic cell cycle, embryonic / cellularization / lipid droplet / ribonucleoprotein complex / RNA binding / cytoplasm / cytosol
Similarity search - Function
Caprin / Caprin-1 dimerization domain / Caprin-1 dimerization domain
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhu, J. / Wu, Y. / Huang, X. / Du, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM116062-01 United States
CitationJournal: To Be Published
Title: Crystal structure of a dimerization domain of Drosophila Caprin: further supports the assembly of an evolutionarily conserved ribonucleoprotein complex containing Caprin and FMRP
Authors: Zhu, J. / Wu, Y. / Huang, X. / Du, Z.
History
DepositionNov 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caprin homolog
B: Caprin homolog


Theoretical massNumber of molelcules
Total (without water)28,5622
Polymers28,5622
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-14 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.050, 60.040, 99.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Caprin homolog


Mass: 14280.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Capr, CG18811 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I7D3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 18% PEG2000, 0.1 M BisTris (pH6.8), 5% glycerol / PH range: 7.0-7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→36.27 Å / Num. all: 30126 / Num. obs: 30126 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 32.65 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.069 / Rsym value: 0.061 / Net I/av σ(I): 6.1 / Net I/σ(I): 13.9 / Num. measured all: 153362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.95.10.4951.643580.240.5520.495100
1.9-2.015.10.2742.741030.1320.3050.274100
2.01-2.155.10.1445.138610.0690.160.144100
2.15-2.325.10.0987.136210.0470.1090.098100
2.32-2.555.20.0689.833360.0330.0760.068100
2.55-2.855.10.0629.930450.030.0690.062100
2.85-3.295.10.05610.126820.0270.0620.056100
3.29-4.025.10.078.623180.0340.0780.07100
4.02-5.6950.04113.818120.020.0460.041100
5.69-60.044.30.03713.39900.020.0430.03792.7

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Processing

Software
NameVersionClassification
MOSFLMdata collection
SCALA3.3.22data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WBE

4wbe


Resolution: 1.8→36.27 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.67
RfactorNum. reflection% reflection
Rfree0.2453 1999 6.65 %
Rwork0.2146 --
obs0.2167 30061 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 80.01 Å2 / Biso mean: 35.1073 Å2 / Biso min: 16.85 Å2
Refinement stepCycle: final / Resolution: 1.8→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 0 75 1714
Biso mean---35.95 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061659
X-RAY DIFFRACTIONf_angle_d0.6872228
X-RAY DIFFRACTIONf_chiral_restr0.044253
X-RAY DIFFRACTIONf_plane_restr0.003290
X-RAY DIFFRACTIONf_dihedral_angle_d12.4221012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8450.3141420.272519882130100
1.845-1.89490.29451420.254319932135100
1.8949-1.95070.27791390.238519662105100
1.9507-2.01360.27371420.214119792121100
2.0136-2.08560.25631410.199519762117100
2.0856-2.16910.23411420.198119942136100
2.1691-2.26780.24611410.202119772118100
2.2678-2.38730.23851420.196220022144100
2.3873-2.53690.24651430.196219992142100
2.5369-2.73270.2461430.203220042147100
2.7327-3.00760.24451440.207920132157100
3.0076-3.44250.24591440.217520292173100
3.4425-4.3360.22011470.201820652212100
4.336-36.27710.25591470.24072077222496
Refinement TLS params.Method: refined / Origin x: 43.6037 Å / Origin y: 32.6668 Å / Origin z: 32.3529 Å
111213212223313233
T0.2058 Å2-0.0084 Å2-0.0098 Å2-0.2337 Å2-0.0057 Å2--0.2251 Å2
L0.9542 °20.1209 °2-0.2286 °2-1.5225 °20.4693 °2--0.8065 °2
S0.0815 Å °-0.0883 Å °-0.1468 Å °0.0751 Å °-0.1461 Å °0.0262 Å °-0.0386 Å °-0.198 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA194 - 305
2X-RAY DIFFRACTION1allB194 - 308
3X-RAY DIFFRACTION1allS2 - 187

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