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- PDB-3qjp: An RAMP protein binding different RNA substrates -

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Basic information

Entry
Database: PDB / ID: 3qjp
TitleAn RAMP protein binding different RNA substrates
Components
  • Putative uncharacterized protein PH0350
  • RNA (5'-R(P*UP*AP*GP*UP*UP*UP*AP*A)-3')
KeywordsIMMUNE SYSTEM/RNA / Ferridoxin-fold / work in immune system in prokaryotes / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / defense response to virus / RNA binding
Similarity search - Function
: / CRISPR associated protein Cas6, C-terminal / CRISPR-associated protein Cas6, N-terminal / Alpha-Beta Plaits - #1890 / CRISPR-associated protein Cas6, N-terminal domain superfamily / Alpha-Beta Plaits - #1900 / CRISPR-associated protein, Cas6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Putative CRISPR-associated endoribonuclease-like protein Cas6nc
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2986 Å
AuthorsWang, R. / Zheng, H. / Preamplume, G. / Li, H.
CitationJournal: To be Published
Title: Cooperative and Specific Binding of a RAMP Protein to Single-stranded CRISPR Repeat RNA
Authors: Wang, R. / Zheng, H. / Preamplume, G. / Li, H.
History
DepositionJan 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: RNA (5'-R(P*UP*AP*GP*UP*UP*UP*AP*A)-3')
A: Putative uncharacterized protein PH0350


Theoretical massNumber of molelcules
Total (without water)30,4422
Polymers30,4422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-5 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.781, 76.781, 193.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain RNA (5'-R(P*UP*AP*GP*UP*UP*UP*AP*A)-3')


Mass: 2512.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CRISPR
#2: Protein Putative uncharacterized protein PH0350


Mass: 27929.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH0350 / References: UniProt: O58088

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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: 4.68 Å3/Da / Density % sol: 73.71 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.01 M MgSO4, 0.05 M Na Cacodylate (pH6.0), and 1.8 M Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5621 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5621 Å / Relative weight: 1
ReflectionResolution: 3.2986→50 Å / Num. all: 9254 / Num. obs: 9254 / % possible obs: 83 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_589) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2986→30.295 Å / SU ML: 0.45 / σ(F): 0 / Phase error: 26.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 896 10.04 %
Rwork0.2267 --
obs0.2312 8928 96.25 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.24 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.2986→30.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 169 0 0 2116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082176
X-RAY DIFFRACTIONf_angle_d1.3592965
X-RAY DIFFRACTIONf_dihedral_angle_d21.398858
X-RAY DIFFRACTIONf_chiral_restr0.086337
X-RAY DIFFRACTIONf_plane_restr0.005344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2986-3.5050.40381280.34461167X-RAY DIFFRACTION86
3.505-3.77510.36861460.29061279X-RAY DIFFRACTION96
3.7751-4.15420.3051510.23591316X-RAY DIFFRACTION97
4.1542-4.75330.21871520.16891374X-RAY DIFFRACTION99
4.7533-5.98110.24781520.21131394X-RAY DIFFRACTION99
5.9811-30.29660.25621670.22861502X-RAY DIFFRACTION100

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