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- PDB-3qjj: One RAMP protein binding different RNA substrates -

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Basic information

Entry
Database: PDB / ID: 3qjj
TitleOne RAMP protein binding different RNA substrates
Components
  • Putative uncharacterized protein PH0350
  • RNA (5'-R(*GP*UP*UP*GP*AP*AP*AP*UP*CP*AP*GP*A)-3')
KeywordsIMMUNE SYSTEM/RNA / Single-stranded RNA binding / 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 domain superfamily / Alpha-Beta Plaits - #1890 / Alpha-Beta Plaits - #1900 / CRISPR-associated protein, Cas6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Putative CRISPR-associated endoribonuclease-like protein Cas6nc
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8049 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 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,8564
Polymers63,8564
Non-polymers00
Water0
1
R: RNA (5'-R(*GP*UP*UP*GP*AP*AP*AP*UP*CP*AP*GP*A)-3')
B: Putative uncharacterized protein PH0350


Theoretical massNumber of molelcules
Total (without water)31,9282
Polymers31,9282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-1 kcal/mol
Surface area12230 Å2
MethodPISA
2
A: Putative uncharacterized protein PH0350
Q: RNA (5'-R(*GP*UP*UP*GP*AP*AP*AP*UP*CP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)31,9282
Polymers31,9282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-4 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.269, 75.269, 257.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 3860.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CRISPR
#2: Protein Putative uncharacterized protein PH0350


Mass: 28067.678 Da / Num. of mol.: 2
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: 2

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.005 M MgSO4, 0.05 M MES (pH6.0), 3-8% PEG4000, 0.2 M NaCl and 0.1 M KCl, pH 7.0, 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
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5621 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 18997 / Num. obs: 18997 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: dev_589)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8049→37.266 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 1853 10 %
Rwork0.2111 --
obs0.2162 18537 97.44 %
all-19024 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.397 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0547 Å2-0 Å20 Å2
2---3.0547 Å20 Å2
3---6.1094 Å2
Refinement stepCycle: LAST / Resolution: 2.8049→37.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 512 0 0 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144583
X-RAY DIFFRACTIONf_angle_d1.8446287
X-RAY DIFFRACTIONf_dihedral_angle_d17.3371819
X-RAY DIFFRACTIONf_chiral_restr0.102715
X-RAY DIFFRACTIONf_plane_restr0.012702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8049-2.88080.41081320.32691179X-RAY DIFFRACTION93
2.8808-2.96550.35111340.28131209X-RAY DIFFRACTION95
2.9655-3.06120.33861400.26221237X-RAY DIFFRACTION96
3.0612-3.17050.29471370.25241249X-RAY DIFFRACTION97
3.1705-3.29740.31991360.24671262X-RAY DIFFRACTION98
3.2974-3.44740.30571410.23191280X-RAY DIFFRACTION98
3.4474-3.6290.29921410.21981242X-RAY DIFFRACTION96
3.629-3.85610.29941390.20791236X-RAY DIFFRACTION95
3.8561-4.15350.26561440.18481296X-RAY DIFFRACTION99
4.1535-4.57080.1831470.16161320X-RAY DIFFRACTION100
4.5708-5.23070.19781480.16751335X-RAY DIFFRACTION100
5.2307-6.58410.28721510.22241368X-RAY DIFFRACTION100
6.5841-37.26920.22941630.21551471X-RAY DIFFRACTION100

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