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- PDB-1whi: RIBOSOMAL PROTEIN L14 -

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Basic information

Entry
Database: PDB / ID: 1whi
TitleRIBOSOMAL PROTEIN L14
ComponentsRIBOSOMAL PROTEIN L14
KeywordsRIBOSOMAL PROTEIN / RRNA-BINDING
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal protein L14P, bacterial-type / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL14
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsDavies, C. / White, S.W. / Ramakrishnan, V.
Citation
Journal: Structure / Year: 1996
Title: The crystal structure of ribosomal protein L14 reveals an important organizational component of the translational apparatus.
Authors: Davies, C. / White, S.W. / Ramakrishnan, V.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction of Bacterial Ribosomal Protein L14
Authors: Davies, C. / Gerchman, S.E. / Kycia, J.H. / Mcgee, K. / Ramakrishnan, V. / White, S.W.
History
DepositionJan 10, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN L14


Theoretical massNumber of molelcules
Total (without water)13,3701
Polymers13,3701
Non-polymers00
Water1,874104
1
A: RIBOSOMAL PROTEIN L14

A: RIBOSOMAL PROTEIN L14


Theoretical massNumber of molelcules
Total (without water)26,7392
Polymers26,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)66.900, 32.700, 49.400
Angle α, β, γ (deg.)90.00, 101.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RIBOSOMAL PROTEIN L14


Mass: 13369.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Description: T7 EXPRESSION SYSTEM INDUCIBLE BY ISOPROPYL-BETA-D-THIOGALACTOPYRANOSIDE (IPTG)
Cell line: BL21 / Gene: BACILLUS STEAROTHERMOPHILUS / Plasmid: PET13
Gene (production host): BACILLUS STEAROTHERMOPHILUS (ACCESSION P04450)
Production host: Escherichia coli (E. coli) / References: UniProt: P04450
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.98 Å3/Da / Density % sol: 38.2 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop
Details: Davies, C., (1994) Acta Crystallogr.,Sect.D, 50, 790.
Components of the solutions
*PLUS
Conc.: 1.0-1.5 M / Common name: sodium citrate

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→14.6 Å / Num. obs: 15965 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 2.44 % / Rmerge(I) obs: 0.042

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.5→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.255 -10 %
Rwork0.189 --
obs0.189 15877 94 %
Displacement parametersBiso mean: 13.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1137 0 0 103 1240
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.03
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.947
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.261
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.947

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