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

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Basic information

Entry
Database: PDB / ID: 3qjl
TitleOne RAMP protein binding different RNA substrates
Components
  • Putative uncharacterized protein PH0350
  • RNA (5'-R(*GP*UP*UP*AP*CP*AP*AP*UP*AP*AP*GP*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 / RNA (> 10) / Putative CRISPR-associated endoribonuclease-like protein Cas6nc
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7009 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_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)63,8244
Polymers63,8244
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-6 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.773, 88.773, 257.629
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: 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
#2: RNA chain RNA (5'-R(*GP*UP*UP*AP*CP*AP*AP*UP*AP*AP*GP*A)-3')


Mass: 3844.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CRISPR
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.005 M MgSO4, 0.05 M MES (pH6.0), 3-8% PEG4000, 0.2 M NaCl and 0.1 M KCl, 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: 28452 / Num. obs: 28452 / % possible obs: 89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→50 Å / % possible all: 89

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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: 2.7009→39.7 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 1861 7.03 %
Rwork0.2184 --
obs0.2216 26485 90.59 %
all-29236 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.466 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.3413 Å20 Å2-0 Å2
2--13.3413 Å2-0 Å2
3----26.6826 Å2
Refinement stepCycle: LAST / Resolution: 2.7009→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 510 0 39 4443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074548
X-RAY DIFFRACTIONf_angle_d1.1526238
X-RAY DIFFRACTIONf_dihedral_angle_d17.9941810
X-RAY DIFFRACTIONf_chiral_restr0.08712
X-RAY DIFFRACTIONf_plane_restr0.006696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7009-2.7740.4685920.39261228X-RAY DIFFRACTION60
2.774-2.85560.48691120.35521435X-RAY DIFFRACTION71
2.8556-2.94770.40651220.31171643X-RAY DIFFRACTION80
2.9477-3.0530.31541400.27511882X-RAY DIFFRACTION91
3.053-3.17520.31231430.27431933X-RAY DIFFRACTION94
3.1752-3.31960.33471530.25721982X-RAY DIFFRACTION97
3.3196-3.49460.28321460.24151945X-RAY DIFFRACTION94
3.4946-3.71340.28081500.21532000X-RAY DIFFRACTION97
3.7134-3.99980.25051540.19932008X-RAY DIFFRACTION96
3.9998-4.40190.21931580.17072064X-RAY DIFFRACTION99
4.4019-5.03770.2011580.15652097X-RAY DIFFRACTION99
5.0377-6.34280.22381620.21792148X-RAY DIFFRACTION99
6.3428-39.70480.24881710.21052259X-RAY DIFFRACTION99

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