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- PDB-1dd3: CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L12 FROM THERMOTOGA MARITIMA -

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Basic information

Entry
Database: PDB / ID: 1dd3
TitleCRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN L12 FROM THERMOTOGA MARITIMA
Components(50S RIBOSOMAL PROTEIN L7/L12Ribosome) x 2
KeywordsRIBOSOME / DIMER FORMATION / FLEXIBILITY / HINGE REGION / FOUR-HELIX-BUNDLE / FIVE-HELIX- BUNDLE / ALPHA-BETA STRUCTURE / HELICAL HAIRPIN / DOMAINS
Function / homology
Function and homology information


cytosolic large ribosomal subunit / structural constituent of ribosome / translation / mRNA binding
Similarity search - Function
Single helix bin / Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / 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 L30; Chain: A, / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like ...Single helix bin / Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / 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 L30; Chain: A, / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein bL12
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWahl, M.C. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R.
CitationJournal: EMBO J. / Year: 2000
Title: Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12.
Authors: Wahl, M.C. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R.
History
DepositionNov 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 14, 2016Group: Other
Revision 1.4Dec 18, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value
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

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L7/L12
B: 50S RIBOSOMAL PROTEIN L7/L12
C: 50S RIBOSOMAL PROTEIN L7/L12
D: 50S RIBOSOMAL PROTEIN L7/L12


Theoretical massNumber of molelcules
Total (without water)34,1714
Polymers34,1714
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-70 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.330, 89.130, 119.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L7/L12 / Ribosome


Mass: 13475.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermotoga maritima (bacteria) / References: UniProt: P29396
#2: Protein/peptide 50S RIBOSOMAL PROTEIN L7/L12 / Ribosome


Mass: 3610.214 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermotoga maritima (bacteria) / References: UniProt: P29396
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 3.6M AMMOMIUM SULFATE 0.1M SODIUM CITRATE 7% (V/V) POLYETHYLENE GLYCOL 200, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
27.1 mMHEPES1drop
30.692 Mammonium sulfate1drop
40.02 Msodium citrate1drop
52.1 %PEG2001drop
63.23 Mammonium sulfate1reservoir
70.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 20359 / Num. obs: 20073 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 22.1
Reflection shellResolution: 2→2.1 Å
Reflection
*PLUS
Redundancy: 3.7 %
Reflection shell
*PLUS
% possible obs: 95.1 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→6 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1004 -RANDOM
Rwork0.226 ---
obs0.226 18554 98.6 %-
all-18554 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.735 Å20 Å20 Å2
2--9.533 Å20 Å2
3----1.798 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 0 247 2637
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.35
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
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.71
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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