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- PDB-1vi6: Crystal structure of ribosomal protein S2P -

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Basic information

Entry
Database: PDB / ID: 1vi6
TitleCrystal structure of ribosomal protein S2P
Components30S ribosomal protein S2PRibosome
KeywordsRIBOSOME / structural genomics
Function / homology
Function and homology information


small ribosomal subunit / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein S2, archaeal / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S2 signature 2. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Rossmann fold ...Ribosomal protein S2, archaeal / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S2 signature 2. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ribosomal subunit protein uS2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry / _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 S2P
B: 30S ribosomal protein S2P
C: 30S ribosomal protein S2P
D: 30S ribosomal protein S2P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,13314
Polymers93,9034
Non-polymers23010
Water10,052558
1
A: 30S ribosomal protein S2P
B: 30S ribosomal protein S2P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0677
Polymers46,9522
Non-polymers1155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 30S ribosomal protein S2P
D: 30S ribosomal protein S2P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0677
Polymers46,9522
Non-polymers1155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.829, 123.829, 131.949
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
30S ribosomal protein S2P / Ribosome


Mass: 23475.857 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: RPS2P, AF1133 / Production host: Escherichia coli (E. coli) / References: UniProt: O29132
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→36.48 Å / Num. all: 87095 / Num. obs: 87095 / % possible obs: 99.1 % / Redundancy: 14 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 4.2 / % possible all: 93.6
Reflection
*PLUS
Rmerge(I) obs: 0.12
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMAC4refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→36.48 Å / σ(F): 0
RfactorNum. reflection
Rfree0.243 3748
Rwork0.208 -
obs-75042
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 330.468 Å2 / ksol: 0.999 e/Å3
Displacement parametersBiso mean: 24.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.581 Å20 Å20 Å2
2--0.581 Å20 Å2
3----1.163 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.95→36.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6119 0 10 558 6687
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d1.362
X-RAY DIFFRACTIONp_planar_tor1.217
X-RAY DIFFRACTIONp_chiral_restr0.099
X-RAY DIFFRACTIONp_plane_restr0.005
X-RAY DIFFRACTIONp_mcbond_it1.941
X-RAY DIFFRACTIONp_mcangle_it3.158
X-RAY DIFFRACTIONp_scbond_it3.326
X-RAY DIFFRACTIONp_scangle_it4.829
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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