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- PDB-1vmb: Crystal structure of 30S ribosomal protein S6 (TM0603) from Therm... -

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Basic information

Entry
Database: PDB / ID: 1vmb
TitleCrystal structure of 30S ribosomal protein S6 (TM0603) from Thermotoga maritima at 1.70 A resolution
Components30S ribosomal protein S6
KeywordsTRANSLATION / TM0603 / 30S RIBOSOMAL PROTEIN S6 / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cytoplasm
Similarity search - Function
Ribosomal protein S6/Translation elongation factor EF1B / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 30S ribosomal protein S6 (TM0603) from Thermotoga maritima at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 30S ribosomal protein S6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9813
Polymers16,8571
Non-polymers1242
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.815, 60.815, 76.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

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Components

#1: Protein 30S ribosomal protein S6


Mass: 16857.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rpsF,TM0603 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ72
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.37 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 20.0% PEG-3350, 0.1M NaAcetate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.980075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2004 / Details: flat mirror
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980075 Å / Relative weight: 1
ReflectionResolution: 1.7→47.62 Å / Num. obs: 15840 / % possible obs: 96.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 29.25 Å2 / Rsym value: 0.073 / Net I/σ(I): 16.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 880 / Rsym value: 0.391 / % possible all: 73.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC(5.2.0001)refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lou

1lou


Resolution: 1.7→47.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.859 / SU ML: 0.067 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23735 788 5 %RANDOM
Rwork0.18287 ---
obs0.18549 15000 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.517 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 0 8 114 1044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022965
X-RAY DIFFRACTIONr_bond_other_d0.0030.02906
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.951285
X-RAY DIFFRACTIONr_angle_other_deg0.92732097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7675106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.34523.05159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85515199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1321514
X-RAY DIFFRACTIONr_chiral_restr0.1060.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
X-RAY DIFFRACTIONr_nbd_refined0.2050.2174
X-RAY DIFFRACTIONr_nbd_other0.2020.2983
X-RAY DIFFRACTIONr_nbtor_other0.0830.2582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0620.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.218
X-RAY DIFFRACTIONr_mcbond_it1.321.5590
X-RAY DIFFRACTIONr_mcbond_other0.3511.5217
X-RAY DIFFRACTIONr_mcangle_it1.5772878
X-RAY DIFFRACTIONr_scbond_it2.8323469
X-RAY DIFFRACTIONr_scangle_it4.0714.5407
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 38 4.34 %
Rwork0.229 838 -
Refinement TLS params.Method: refined / Origin x: 25.2294 Å / Origin y: 7.889 Å / Origin z: 32.502 Å
111213212223313233
T-0.1565 Å20.0243 Å20.0114 Å2--0.1452 Å20.01 Å2---0.1248 Å2
L2.0927 °20.7822 °2-0.3684 °2-2.294 °20.0167 °2--2.6834 °2
S-0.016 Å °0.0407 Å °0.1192 Å °-0.0173 Å °0.0025 Å °0.0787 Å °-0.1184 Å °-0.1311 Å °0.0135 Å °
Refinement TLS groupSelection: ALL

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