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- PDB-2j5a: Folding of S6 structures with divergent amino-acid composition: p... -

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Basic information

Entry
Database: PDB / ID: 2j5a
TitleFolding of S6 structures with divergent amino-acid composition: pathway flexibility within partly overlapping foldons
Components30S RIBOSOMAL PROTEIN S6
KeywordsRNA-BINDING / AQUIFEX AEOLICUS / RIBOSOMAL PROTEIN / RIBONUCLEOPROTEIN / RIBOSOMAL PROTEIN S6 / RRNA-BINDING / PROTEIN FOLDING
Function / homology
Function and homology information


small ribosomal subunit rRNA binding / ribosome / structural constituent of 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 speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHansson, S. / Olofsson, L. / Hedberg, L. / Oliveberg, M. / Logan, D.T.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Folding of S6 Structures with Divergent Amino Acid Composition: Pathway Flexibility within Partly Overlapping Foldons.
Authors: Olofsson, M. / Hansson, S. / Hedberg, L. / Logan, D.T. / Oliveberg, M.
History
DepositionSep 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 30S RIBOSOMAL PROTEIN S6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4822
Polymers13,4591
Non-polymers231
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.570, 75.570, 55.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 30S RIBOSOMAL PROTEIN S6 / RIBOSOMAL PROTEIN S6


Mass: 13459.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66474
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE AT POSITION 98 HAS BEEN MODELLED AS ILE ON THE BASIS OF FIT TO ELECTRON DENSITY. THIS ...THE RESIDUE AT POSITION 98 HAS BEEN MODELLED AS ILE ON THE BASIS OF FIT TO ELECTRON DENSITY. THIS HAS NOT BEEN CONFIRMED INDEPENDENTLY, E.G. BY SEQUENCING OF THE OVEREXPRESSION PLASMID. HOWEVER, THE FIT FOR PHE WAS POOR AND THE DENSITY HAS THE APPEARANCE OF ILE.

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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: 3.75 Å3/Da / Density % sol: 62.4 %
Description: BETA VERSION OF PHASER STRUCTURE SOLVED USING A PRELIMINARY 2.6A DATA SET
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP 14% POLYETHYLENE GLYCOL 3350, 0.2M NA FORMATE, 4UL PROTEIN, 4UL RESERVOIR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→28.2 Å / Num. obs: 8252 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.2 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G1X

1g1x


Resolution: 2.3→25.55 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.568 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 381 4.68 %RANDOM
Rwork0.223 ---
obs0.225 8250 98.2 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 37.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.017 Å20.508 Å20 Å2
2--1.017 Å20 Å2
3----1.525 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 1 45 962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9591258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7535105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.80125.38552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59115188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.391154
X-RAY DIFFRACTIONr_chiral_restr0.0810.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021010
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2176
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.27
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1322004
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8121.5530
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5342862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8183422
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0074.5396
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 26
Rwork0.248 571
Refinement TLS params.Method: refined / Origin x: -0.862 Å / Origin y: 34.332 Å / Origin z: 16.232 Å
111213212223313233
T-0.073 Å20.0237 Å2-0.0139 Å2--0.0775 Å20.0094 Å2---0.0821 Å2
L4.1179 °20.0832 °20.7086 °2-0.6171 °2-0.0193 °2--2.1042 °2
S-0.1353 Å °-0.1863 Å °-0.0607 Å °-0.0751 Å °0.0784 Å °0.0639 Å °0.067 Å °0.0114 Å °0.057 Å °

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