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- PDB-1v8q: Crystal structure of ribosomal protein L27 from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 1v8q
TitleCrystal structure of ribosomal protein L27 from Thermus thermophilus HB8
ComponentsTT0826
KeywordsTRANSLATION / structural genomics / proteomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation
Similarity search - Function
RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L27 / Ribosomal L27 protein / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Large ribosomal subunit protein bL27 / 50S ribosomal protein L27
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsWang, H. / Takemoto-Hori, C. / Murayama, K. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2004
Title: Crystal structure of ribosomal protein L27 from Thermus thermophilus HB8
Authors: Wang, H. / Takemoto-Hori, C. / Murayama, K. / Sakai, H. / Tatsuguchi, A. / Terada, T. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJan 13, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: TT0826
B: TT0826
C: TT0826
D: TT0826
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2715
Polymers38,1164
Non-polymers1541
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.543, 48.543, 139.120
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
TT0826


Mass: 9529.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET-26 / Production host: Escherichia coli (E. coli) / References: UniProt: P84123, UniProt: P60493*PLUS
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, Ammonium Acetate, tri-Sodium Citrate dihydrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44B210.9
SYNCHROTRONSPring-8 BL26B120.96000, 0.97854, 0.97934, 0.98454
Detector
TypeIDDetectorDate
MACSCIENCE1CCDFeb 25, 2002
RIGAKU2IMAGE PLATEDec 13, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.961
30.978541
40.979341
50.984541
ReflectionResolution: 2.8→45.83 Å / Num. obs: 7947 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 48.7 Å2 / Rsym value: 0.074 / Net I/σ(I): 27.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 766 / Rsym value: 0.43 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→45.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 237937.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 802 10.7 %RANDOM
Rwork0.197 ---
obs0.197 7520 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.2951 Å2 / ksol: 0.389673 e/Å3
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1-16.44 Å20 Å20 Å2
2--16.44 Å20 Å2
3----32.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 8 18 2142
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 99 9.1 %
Rwork0.32 993 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3DTT_CNS.PARAM

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