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- PDB-3aqq: Crystal structure of human CRHSP-24 -

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Basic information

Entry
Database: PDB / ID: 3aqq
TitleCrystal structure of human CRHSP-24
ComponentsCalcium-regulated heat stable protein 1
KeywordsDNA BINDING PROTEIN / compact beta-barrel / Cold shock domain / ssDNA binding
Function / homology
Function and homology information


cytoplasmic exosome (RNase complex) / P granule / phosphatase binding / regulation of mRNA stability / mRNA 3'-UTR binding / P-body / intracellular signal transduction / cytosol / cytoplasm
Similarity search - Function
Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold ...Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Calcium-regulated heat-stable protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.798 Å
AuthorsHou, H. / Wang, F. / Zhang, W. / Wang, D. / Li, X. / Bartlam, M. / Yao, X. / Rao, Z.
CitationJournal: To be Published
Title: CRHSP-24 is a novel cargo adaptor trafficking between stress granules and processing bodies
Authors: Hou, H. / Wang, F. / Zhang, W. / Wang, D. / Li, X. / Bartlam, M. / Yao, X. / Rao, Z.
History
DepositionNov 17, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-regulated heat stable protein 1
C: Calcium-regulated heat stable protein 1
B: Calcium-regulated heat stable protein 1
D: Calcium-regulated heat stable protein 1


Theoretical massNumber of molelcules
Total (without water)63,6564
Polymers63,6564
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-19 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.856, 79.856, 181.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Calcium-regulated heat stable protein 1 / Calcium-regulated heat-stable protein of 24 kDa / CRHSP-24


Mass: 15914.057 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARHSP1 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y2V2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 0.1M sodium acetate trihydrate, 2.0M sodium formate, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2008
RadiationMonochromator: LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.798→50 Å / Num. obs: 16210 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.798→45.603 Å / SU ML: 0.39 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2724 812 5.03 %
Rwork0.2285 --
obs0.2307 16140 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.072 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.1167 Å2-0 Å2-0 Å2
2--8.1167 Å20 Å2
3----16.2334 Å2
Refinement stepCycle: LAST / Resolution: 2.798→45.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 0 32 3048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083093
X-RAY DIFFRACTIONf_angle_d1.2664187
X-RAY DIFFRACTIONf_dihedral_angle_d18.0931120
X-RAY DIFFRACTIONf_chiral_restr0.079468
X-RAY DIFFRACTIONf_plane_restr0.006537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7985-2.97380.36481630.27842526X-RAY DIFFRACTION99
2.9738-3.20330.32661250.24292568X-RAY DIFFRACTION100
3.2033-3.52560.29061290.24422535X-RAY DIFFRACTION100
3.5256-4.03540.25151570.21012548X-RAY DIFFRACTION100
4.0354-5.08320.24671140.19442580X-RAY DIFFRACTION100
5.0832-45.60940.23571240.23562571X-RAY DIFFRACTION99

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