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- PDB-1dmg: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L4 -

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Basic information

Entry
Database: PDB / ID: 1dmg
TitleCRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L4
ComponentsRIBOSOMAL PROTEIN L4
KeywordsGENE REGULATION / ALPHA-BETA / RIBOSOMAL PROTEIN / L4 / RIBOSOME / RNA / S10 OPERON
Function / homology
Function and homology information


rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / DNA binding
Similarity search - Function
Ribosomal Protein L4; Chain: A; / Ribosomal protein L4/L1 / 50S ribosomal protein uL4 / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Large ribosomal subunit protein uL4
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsWorbs, M. / Huber, R. / Wahl, M.C.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of ribosomal protein L4 shows RNA-binding sites for ribosome incorporation and feedback control of the S10 operon.
Authors: Worbs, M. / Huber, R. / Wahl, M.C.
History
DepositionDec 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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

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Assembly

Deposited unit
A: RIBOSOMAL PROTEIN L4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8832
Polymers25,6911
Non-polymers1921
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.000, 48.600, 112.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RIBOSOMAL PROTEIN L4


Mass: 25690.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET22B+ / Production host: Escherichia coli (E. coli) / References: UniProt: P38516
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: PEG400, AMMONIUM ACETATE, CITRATE, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.4 mg/mlprotein1drop
210 mMHEPES1drop
3100 mMcitrate1reservoir
435-38 %PEG4001reservoir
5200 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.7→15 Å / Num. all: 25013 / Num. obs: 23468 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 25.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2 % / Rmerge(I) obs: 0.32 / % possible all: 88
Reflection shell
*PLUS
% possible obs: 88 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.237 1106 RANDOM
Rwork0.208 --
obs0.208 22806 -
all-23234 -
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 13 213 1623
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.5
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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