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- PDB-1pxw: Crystal structure of L7Ae sRNP core protein from Pyrococcus abyssii -

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Basic information

Entry
Database: PDB / ID: 1pxw
TitleCrystal structure of L7Ae sRNP core protein from Pyrococcus abyssii
ComponentsLSU ribosomal protein L7AE
KeywordsRIBOSOME
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm
Similarity search - Function
Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein eL8
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsCharron, C. / Manival, X. / Charpentier, B. / Branlant, C. / Aubry, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Purification, crystallization and preliminary X-ray diffraction data of L7Ae sRNP core protein from Pyrococcus abyssii.
Authors: Charron, C. / Manival, X. / Charpentier, B. / Branlant, C. / Aubry, A.
History
DepositionJul 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LSU ribosomal protein L7AE
B: LSU ribosomal protein L7AE


Theoretical massNumber of molelcules
Total (without water)28,1552
Polymers28,1552
Non-polymers00
Water2,396133
1
A: LSU ribosomal protein L7AE


Theoretical massNumber of molelcules
Total (without water)14,0771
Polymers14,0771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LSU ribosomal protein L7AE


Theoretical massNumber of molelcules
Total (without water)14,0771
Polymers14,0771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.190, 112.550, 34.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein LSU ribosomal protein L7AE


Mass: 14077.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P62008
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PEG MME 2000, magnesium chloride, sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
2300 mM1dropNaCl
320 mMTris-HCl1droppH8.0
420 %(v/v)PEG2000 MME1reservoir
5160 mM1reservoirMgCl2
6100 mMsodium acetate1reservoirpH4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.94→15 Å / Num. all: 19168 / Num. obs: 19168 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.94→2.03 Å / % possible all: 68.6
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / Num. obs: 5958 / % possible obs: 91 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.084 / Num. measured all: 18984
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 77.5 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 932 RANDOM
Rwork0.227 --
all0.229 19168 -
obs0.229 19168 -
Refinement stepCycle: LAST / Resolution: 1.94→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1903 0 0 133 2036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.233
LS refinement shellResolution: 1.94→2.03 Å
RfactorNum. reflection% reflection
Rfree0.332 72 -
Rwork0.254 --
obs-1696 68.6 %

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