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- PDB-1ctf: STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RIBOSOMAL PROTEIN L7/L1... -

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Basic information

Entry
Database: PDB / ID: 1ctf
TitleSTRUCTURE OF THE C-TERMINAL DOMAIN OF THE RIBOSOMAL PROTEIN L7/L12 FROM ESCHERICHIA COLI AT 1.7 ANGSTROMS
ComponentsRIBOSOMAL PROTEIN L7/L12
KeywordsRIBOSOMAL PROTEIN
Function / homology
Function and homology information


large ribosomal subunit / ribosome binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation / mRNA binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein bL12
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsLeijonmarck, M. / Liljas, A.
Citation
Journal: J Mol Biol / Year: 1987
Title: Structure of the C-terminal domain of the ribosomal protein L7/L12 from Escherichia coli at 1.7 A.
Authors: M Leijonmarck / A Liljas /
Abstract: The structure of a C-terminal fragment of the ribosomal protein L7/L12 from Escherichia coli has been refined using crystallographic data to 1.7 A resolution. The R-value is 17.4%. Six residues at ...The structure of a C-terminal fragment of the ribosomal protein L7/L12 from Escherichia coli has been refined using crystallographic data to 1.7 A resolution. The R-value is 17.4%. Six residues at the N terminus are too disordered in the structure to be localized. These residues are probably part of a hinge in the complete L7/L12 molecule. The possibility that a 2-fold crystallographic axis is a molecular 2-fold axis is discussed. A patch of invariant residues on the surface of the dimer is probably involved in functional interactions with elongation factors.
#1: Journal: Structural Aspects of Recognition and Assembly in Biological Macromolecules
Year: 1981
Title: Structural Studies on the Protein L7(Slash)L12 from E. Coli Ribosomes
Authors: Leijonmarck, M. / Pettersson, I. / Liljas, A.
#2: Journal: Nature / Year: 1980
Title: Crystal Structure of a Ribosomal Component at 2.6 Angstroms Resolution
Authors: Leijonmarck, M. / Eriksson, S. / Liljas, A.
#3: Journal: FEBS Lett. / Year: 1978
Title: Isolation and Crystallization of Stable Domains of the Protein L7(Slash)L12 from Escherichia Coli Ribosomes
Authors: Liljas, A. / Eriksson, S. / Donner, D. / Kurland, C.G.
History
DepositionSep 2, 1986Processing site: BNL
Revision 1.0Jan 15, 1987Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN L7/L12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6702
Polymers7,5741
Non-polymers961
Water1,11762
1
A: RIBOSOMAL PROTEIN L7/L12
hetero molecules

A: RIBOSOMAL PROTEIN L7/L12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3394
Polymers15,1472
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)54.830, 54.830, 42.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: THE ELECTRON DENSITY FOR RESIDUE LYS 59 IS POORLY DEFINED FROM CD TO NZ.
2: THE ELECTRON DENSITY FOR RESIDUES LYS 81, LYS 108, LYS 120 IS POORLY DEFINED FROM CG TO NZ.
3: RESIDUE PRO 91 IS A CIS PROLINE.
Components on special symmetry positions
IDModelComponents
11A-160-

HOH

21A-179-

HOH

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Components

#1: Protein RIBOSOMAL PROTEIN L7/L12


Mass: 7573.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0A7K2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal grow
*PLUS
Method: other / Details: Leijonmarck, M., (1980) Nature, 286, 824.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.69 Å / Num. all: 8688 / Num. obs: 7863 / Rmerge(I) obs: 0.018

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Processing

SoftwareName: CORELS / Classification: refinement
RefinementHighest resolution: 1.7 Å /
RfactorNum. reflection
Rwork0.174 -
obs-6617
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms487 0 5 62 554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.025
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Lowest resolution: 6.02 Å / Rfactor all: 0.196 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_plane_restr0.0150.02
X-RAY DIFFRACTIONo_chiral_restr0.19

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