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- PDB-4kc6: Crystal structure of C-terminal deletion mutant of ribosome recyc... -

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Basic information

Entry
Database: PDB / ID: 4kc6
TitleCrystal structure of C-terminal deletion mutant of ribosome recycling factor from Mycobacterium tuberculosis
ComponentsRibosome-recycling factor
KeywordsTRANSLATION / Ribosome recycling / eubacteria / post-termination complex / Elongation factor G / Bacterial cytosol
Function / homology
Function and homology information


translation termination factor activity / ribosomal large subunit binding / translational termination / peptidoglycan-based cell wall / translation / plasma membrane / cytoplasm
Similarity search - Function
Ribosome-recycling factor / Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / 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 / Ribosome recycling factor domain / RRF superfamily / 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
Similarity search - Domain/homology
: / Ribosome-recycling factor / Ribosome-recycling factor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSelvaraj, M. / Govindan, A. / Seshadri, A. / Dubey, B. / Varshney, U. / Vijayan, M.
CitationJournal: J.Biosci. / Year: 2013
Title: Molecular flexibility of Mycobacterium tuberculosis ribosome recycling factor and its functional consequences: an exploration involving mutants.
Authors: Selvaraj, M. / Govindan, A. / Seshadri, A. / Dubey, B. / Varshney, U. / Vijayan, M.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Ribosome-recycling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4463
Polymers20,2211
Non-polymers2252
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.990, 48.790, 84.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosome-recycling factor / RRF / Ribosome-releasing factor


Mass: 20220.938 Da / Num. of mol.: 1 / Mutation: C-terminal deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: frr, MT2949, MTCY274.13c, Rv2882c / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P66734, UniProt: P9WGY1*PLUS
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 298 K / Method: under oil in microbatch plates / pH: 7.8
Details: 6% Polyethylene glycol 4000, 0.1M Tris HCL, 0.6mM Cadmium acetate, 5% polyethylene glycol 400, pH 7.8, Under oil in microbatch plates, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.514 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.4→42.24 Å / Num. obs: 7009 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.124
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 8.2 / Num. unique all: 7009 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WQG

1wqg


Resolution: 2.4→42.21 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 28.575 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.882 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30398 358 5.1 %RANDOM
Rwork0.2508 ---
obs0.25357 6622 99.79 %-
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: 52.26 Å2
Baniso -1Baniso -2Baniso -3
1--4.04 Å20 Å20 Å2
2---3.85 Å2-0 Å2
3---7.89 Å2
Refine analyzeLuzzati coordinate error free: 0.351 Å
Refinement stepCycle: LAST / Resolution: 2.4→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 2 131 1477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191356
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9641832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6575177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.85423.93461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36815242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1311514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021014
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 20 -
Rwork0.399 479 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1765-0.3150.027818.0897.88273.94930.0698-0.04230.0048-0.2756-0.09650.0499-0.1047-0.04290.02670.2478-0.00160.03620.22390.00560.0061-24.5271-3.00444.4673
20.49481.50070.443411.95443.72271.32270.2463-0.1013-0.0151-0.0301-0.2536-0.32320.0206-0.12120.00740.2776-0.02550.04570.2253-0.01760.087-15.1823-3.38017.664
31.0713-0.4449-0.268312.38255.0952.2260.0903-0.04830.0773-0.3501-0.0937-0.1828-0.1009-0.00380.00340.2747-0.00790.00860.24420.03640.0672-17.0284-5.1494-3.1325
42.16330.9202-0.54723.2228-0.39130.852-0.01440.0870.15390.1491-0.0074-0.17360.07010.03280.02190.30790.02210.01570.24770.02510.0368-33.027915.631720.5494
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 29
2X-RAY DIFFRACTION2A103 - 148
3X-RAY DIFFRACTION3A149 - 179
4X-RAY DIFFRACTION4A30 - 102

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