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- PDB-1dd5: CRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTO... -

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Basic information

Entry
Database: PDB / ID: 1dd5
TitleCRYSTAL STRUCTURE OF THERMOTOGA MARITIMA RIBOSOME RECYCLING FACTOR, RRF
ComponentsRIBOSOME RECYCLING FACTOR
KeywordsRIBOSOME / THREE-HELIX BUNDLE / BETA-ALPHA-BETA SANDWICH
Function / homology
Function and homology information


cytoplasmic translational termination / ribosomal large subunit binding / translation / cytosol / cytoplasm
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosome-recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle ...Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosome-recycling factor / Gyrase A; domain 2 - #40 / Topoisomerase I; Chain A, domain 4 / Gyrase A; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Ribosome-recycling factor
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.55 Å
AuthorsSelmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A.
Citation
Journal: Science / Year: 1999
Title: Crystal structure of Thermotoga maritima ribosome recycling factor: a tRNA mimic.
Authors: Selmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-ray Analysis of Thermotoga Maritima Ribosome Recycling Factor
Authors: Selmer, M. / Al-Karadaghi, S. / Hirokawa, G. / Kaji, A. / Liljas, A.
#2: Journal: To be Published
Title: Cloning and Overexpression of Thermotoga Maritima RRF
Authors: Atarashi, K. / Kaji, A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSOME RECYCLING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6683
Polymers21,5481
Non-polymers1202
Water1,17165
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)47.250, 47.250, 297.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

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Components

#1: Protein RIBOSOME RECYCLING FACTOR /


Mass: 21548.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q9X1B9
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.86 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: ammonium sulfate, acetate, glycerol , pH 5.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNH4Cl
40.5 mMdithiothreitol1drop
50.1 Msodium acetate1reservoir
62.0 Mammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineDiffraction-IDWavelength (Å)Wavelength
SYNCHROTRONESRF BM1410.9786,0.9788,0.9184
SYNCHROTRONMAX II I71120.947
Detector
TypeDiffraction-IDDetectorDate
MARRESEARCH1IMAGE PLATEMar 27, 1999
MARRESEARCH2IMAGE PLATEJan 13, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97881
30.91841
40.9471
ReflectionResolution: 2.55→30 Å / Num. all: 11927 / Num. obs: 11648 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 27
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.153 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1261 / % possible all: 91.8
Reflection shell
*PLUS
% possible obs: 91.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementResolution: 2.55→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high rms absF: 1478170 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Solved by selenomethionine MAD
RfactorNum. reflection% reflectionSelection details
Rfree0.277 597 5 %RANDOM
Rwork0.23 ---
All0.232 11878 --
Obs0.232 11878 99.3 %-
Solvent computationSolvent model: flat model / Bsol: 23.6 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 0 73 1577
Refine LS restraints
Refinement-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it3.820.75
X-RAY DIFFRACTIONc_mcangle_it5.361
X-RAY DIFFRACTIONc_scbond_it11.212
X-RAY DIFFRACTIONc_scangle_it13.182.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 100 5.2 %
Rwork0.345 1808 -
Obs--99.1 %
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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