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- PDB-1rlg: Molecular basis of Box C/D RNA-protein interaction: co-crystal st... -

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Entry
Database: PDB / ID: 1rlg
TitleMolecular basis of Box C/D RNA-protein interaction: co-crystal structure of the Archaeal sRNP intiation complex
DescriptorPROTEIN/RNA Complex
KeywordsStructural Protein/RNA / PROTEIN-RNA / Structural Protein-RNA COMPLEX
Specimen sourceArchaeoglobus fulgidus / archaea / thermophilic / アーキオグロブス・フルギダス
MethodX-ray diffraction (2.7 Å resolution / MAD)
AuthorsMoore, T. / Zhang, Y. / Fenley, M.O. / Li, H.
CitationSTRUCTURE, 2004, 12, 807-818

STRUCTURE, 2004, 12, 807-818 Yorodumi Papers
Molecular Basis of Box C/D RNA-Protein Interactions; Cocrystal Structure of Archaeal L7Ae and a Box C/D RNA.
Moore, T. / Zhang, Y. / Fenley, M.O. / Li, H.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 25, 2003 / Release: Jun 1, 2004
RevisionDateData content typeGroupProviderType
1.0Jun 1, 2004Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
C: 25-MER
D: 25-MER
A: 50S ribosomal protein L7Ae
B: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)43,0844
Polyers43,0844
Non-polymers00
Water0
#1
C: 25-MER
A: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)21,5422
Polyers21,5422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
#2
D: 25-MER
B: 50S ribosomal protein L7Ae


Theoretical massNumber of molelcules
Total (without water)21,5422
Polyers21,5422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)120.584, 120.584, 120.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP 2 3
DetailsThe biological assembly is packed by a dimmer in the asymmetric unit by the operations of space group P23

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Components

#1: RNA chain25-MER


Mass: 8329.573 Da / Num. of mol.: 2
#2: Polypeptide(L)50S ribosomal protein L7Ae


Mass: 13212.320 Da / Num. of mol.: 2
Source: (gene. exp.) Archaeoglobus fulgidus / archaea / thermophilic / アーキオグロブス・フルギダス
References: UniProt: O29494

Cellular component

Molecular function

Biological process

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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: 3.66 / Density percent sol: 66.12
Crystal growTemp: 303 K / Method: EVAPORATION / pH: 7.5
Details: PEG 400,magnesium acetate, HEPES , pH 7.5, EVAPORATION, temperature 303K
Crystal grow comp
IDNameCrystal IDSol ID
1PEG 40011
2magnesium acetate11
3HEPES11
4H2O11
5PEG 40012
6magnesium acetate12
7H2O12

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Data collection

DiffractionMean temperature: 263 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL11-1 / Synchrotron site: SSRL / Beamline: BL11-1 / Wavelength: 0.99, 1.09, 0.97
DetectorType: FUJI / Detector: CCD / Collection date: Apr 16, 2003
RadiationMonochromator: GRAPHITE / Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
10.991.0
21.091.0
30.971.0
ReflectionB iso Wilson estimate: 80.7 Å2 / D resolution high: 2.7 Å / D resolution low: 29.25 Å / Number obs: 30750 / Observed criterion sigma F: 2 / Observed criterion sigma I: 2 / Percent possible obs: 0.94
Reflection shellHighest resolution: 2.7 Å / Lowest resolution: 2.71 Å / Percent possible all: 54

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefineMethod to determine structure: MAD / R Free selection details: RANDOM / Data cutoff high absF: 324127.19 / Data cutoff high rms absF: 324127.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 33.1653 / Solvent model param ksol: 0.290896
Displacement parametersB iso mean: 61.9 Å2 / Aniso B11: 0 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0 Å2
Least-squares processR factor R free: 0.26 / R factor R free error: 0.005 / R factor R work: 0.235 / R factor all: 0.235 / R factor obs: 0.235 / Highest resolution: 2.7 Å / Lowest resolution: 29.25 Å / Number reflection R free: 2706 / Number reflection all: 30802 / Number reflection obs: 28953 / Percent reflection R free: 9.3 / Percent reflection obs: 94
Refine analyzeLuzzati coordinate error free: 0.47 Å / Luzzati coordinate error obs: 0.41 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.54 Å / Luzzati sigma a obs: 0.51 Å
Refine hist #LASTHighest resolution: 2.7 Å / Lowest resolution: 29.25 Å
Number of atoms included #LASTProtein: 1774 / Nucleic acid: 1078 / Ligand: 0 / Solvent: 0 / Total: 2852
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d2.78
Refine LS shellHighest resolution: 2.7 Å / R factor R free: 0.396 / R factor R free error: 0.021 / R factor R work: 0.379 / Lowest resolution: 2.87 Å / Number reflection R free: 348 / Number reflection R work: 3738 / Total number of bins used: 6 / Percent reflection R free: 8.5 / Percent reflection obs: 78.8
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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