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- PDB-1bxy: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L30 FROM THERMUS THERMOPHI... -

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Basic information

Entry
Database: PDB / ID: 1bxy
TitleCRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L30 FROM THERMUS THERMOPHILUS AT 1.9 A RESOLUTION: CONFORMATIONAL FLEXIBILITY OF THE MOLECULE.
ComponentsPROTEIN (RIBOSOMAL PROTEIN L30)
KeywordsRIBOSOME / RIBOSOMAL PROTEIN / CONFORMATIONAL CHANGES
Function / homology
Function and homology information


cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L30/L7 / Ribosomal Protein L30; Chain: A, / Ribosomal protein L30, bacterial-type / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL30
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFedorov, R. / Nevskaya, N. / Khairullina, A. / Tishchenko, S. / Mikhailov, A. / Garber, M. / Nikonov, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of ribosomal protein L30 from Thermus thermophilus at 1.9 A resolution: conformational flexibility of the molecule.
Authors: Fedorov, R. / Nevskaya, N. / Khairullina, A. / Tishchenko, S. / Mikhailov, A. / Garber, M. / Nikonov, S.
History
DepositionOct 9, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 11, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.5Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RIBOSOMAL PROTEIN L30)
B: PROTEIN (RIBOSOMAL PROTEIN L30)


Theoretical massNumber of molelcules
Total (without water)13,5982
Polymers13,5982
Non-polymers00
Water1,40578
1
A: PROTEIN (RIBOSOMAL PROTEIN L30)


Theoretical massNumber of molelcules
Total (without water)6,7991
Polymers6,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (RIBOSOMAL PROTEIN L30)


Theoretical massNumber of molelcules
Total (without water)6,7991
Polymers6,7991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 63.500, 77.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.5139, -0.7218, -0.4636), (0.7632, 0.6314, -0.1371), (0.3917, -0.2834, 0.8754)
Vector: 31.2233, -31.2572, -30.3064)

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Components

#1: Protein PROTEIN (RIBOSOMAL PROTEIN L30)


Mass: 6799.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: VK1 / Description: CLONED GENE / Gene: RPL30 / Species (production host): Escherichia coli / Gene (production host): RPL30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P74909
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.04 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
20.8 Mammonium sulfate1drop
375 mMTris-HCl1drop
42.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.5
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.9→80 Å / Num. obs: 15544 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 2.3 %
Reflection
*PLUS
Highest resolution: 1.85 Å / Num. obs: 35601 / % possible obs: 82.9 % / Num. measured all: 150778 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 92.7 % / Num. measured obs: 79.4 / Rmerge(I) obs: 0.319

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 --
Rwork0.203 --
obs0.203 13789 94 %
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 0 78 1030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.079
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.6 Å2

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