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- PDB-1iq4: 5S-RRNA BINDING RIBOSOMAL PROTEIN L5 FROM BACILLUS STEAROTHERMOPHILUS -

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Basic information

Entry
Database: PDB / ID: 1iq4
Title5S-RRNA BINDING RIBOSOMAL PROTEIN L5 FROM BACILLUS STEAROTHERMOPHILUS
Components50S RIBOSOMAL PROTEIN L5
KeywordsRNA BINDING PROTEIN / Ribosomal protein / rRNA-binding / RNP motif
Function / homology
Function and homology information


tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex
Similarity search - Function
50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 ...50s Ribosomal Protein L5; Chain: A, / Ribosomal protein L5 / Ribosomal protein L5, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL5
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, molecular replacement / Resolution: 1.8 Å
AuthorsNakashima, T. / Yao, M. / Kawamura, S. / Iwasaki, K. / Kimura, M. / Tanaka, I.
CitationJournal: RNA / Year: 2001
Title: Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.
Authors: Nakashima, T. / Yao, M. / Kawamura, S. / Iwasaki, K. / Kimura, M. / Tanaka, I.
History
DepositionJun 13, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 21, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.5Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L5
B: 50S RIBOSOMAL PROTEIN L5


Theoretical massNumber of molelcules
Total (without water)40,3532
Polymers40,3532
Non-polymers00
Water6,774376
1
A: 50S RIBOSOMAL PROTEIN L5


Theoretical massNumber of molelcules
Total (without water)20,1771
Polymers20,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 50S RIBOSOMAL PROTEIN L5


Theoretical massNumber of molelcules
Total (without water)20,1771
Polymers20,1771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.65, 49.22, 68.93
Angle α, β, γ (deg.)90.0, 117.32, 90.0
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-282-

HOH

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L5


Mass: 20176.713 Da / Num. of mol.: 2 / Mutation: V9L, K10N, V111A, A121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08895
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.612 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG8000, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MHEPES1reservoir
316 %PEG80001reservoir
410 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 252800 / Num. obs: 37507 / % possible obs: 97.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 36.99 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.046 / Net I/σ(I): 7.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.2239 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5384 / Rsym value: 0.203 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 252800 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.239

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Processing

Software
NameVersionClassification
SHARPphasing
SOLVEphasing
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD, molecular replacement / Resolution: 1.8→10 Å / Isotropic thermal model: individual restrained / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 3680 9.6 %RANDOM
Rwork0.2154 ---
all-37123 --
obs-33443 96.9 %-
Solvent computationBsol: 73.86 Å2 / ksol: 0.392 e/Å3
Displacement parametersBiso mean: 41.64 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å20 Å20 Å2
2---6.046 Å20 Å2
3---1.796 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3036 Å0.2503 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2075 Å0.1863 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 0 376 3202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.045
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_dihedral_angle_d21.88
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.525
X-RAY DIFFRACTIONc_mcangle_it2.002
X-RAY DIFFRACTIONc_scbond_it2.443
X-RAY DIFFRACTIONc_scangle_it3.037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection obs% reflection obs (%)
1.8-1.910.34356179.70.3076546597.6
1.91-2.060.29715900.249155780.9596
2.06-2.260.30125740.240955730.9714
2.26-2.590.28686130.235756070.9752
2.59-3.240.2886530.230456070.9781
3.24-100.22866330.210356130.9591
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 9.6 % / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.88
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
% reflection Rfree: 9.7 %

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