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- PDB-4kaw: Crystal structure of ribosome recycling factor mutant R39G from M... -

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Basic information

Entry
Database: PDB / ID: 4kaw
TitleCrystal structure of ribosome recycling factor mutant R39G from Mycobacterium tuberculosis
ComponentsRibosome-recycling factor
KeywordsTRANSLATION / Ribosome recycling / eubacteria / Disassembly / post-termination complex / ribosome / 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: 2.5 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 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Advisory / Data collection / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
X: Ribosome-recycling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8742
Polymers20,7621
Non-polymers1121
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.360, 33.590, 60.890
Angle α, β, γ (deg.)90.00, 112.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20761.521 Da / Num. of mol.: 1 / Mutation: R39G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: frr, MT2949, MTCY274.13c, Rv2882c / Plasmid: pTRC / 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.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 298 K / Method: under oil using microbatch plates / pH: 7.8
Details: 6% Polyethylene glycol 4000, 20mM Tris-HCl (pH 7.8), 0.6mM Cadmium acetate, 5% Polyethylene glycol 400, Under oil using microbatch plates, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 2, 2006 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.5→51.64 Å / Num. obs: 7487 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 7.7 / Num. unique all: 7487 / % possible all: 99.6

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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: 2.5→33.61 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.874 / SU B: 20.68 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.656 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 342 4.6 %RANDOM
Rwork0.23451 ---
obs0.23637 7138 99.4 %-
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: 50.122 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å2-2.3 Å2
2---0.61 Å20 Å2
3---0.33 Å2
Refine analyzeLuzzati coordinate error free: 0.656 Å
Refinement stepCycle: LAST / Resolution: 2.5→33.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 1 89 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191403
X-RAY DIFFRACTIONr_angle_refined_deg1.0691.9681895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3395182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69224.0367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35215247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1471515
X-RAY DIFFRACTIONr_chiral_restr0.060.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211065
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 21 -
Rwork0.329 540 -
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)
113.28885.353613.91722.30495.782614.86250.02660.2003-0.48750.00350.2917-0.11880.05260.3966-0.31820.22560.04620.03780.37840.0090.282428.382311.045234.0063
21.9466-2.4614-3.95176.57072.157110.4181-0.30090.0299-0.00760.43040.1594-0.24790.5118-0.0420.14150.07950.03180.0680.7431-0.15960.259953.53569.358247.1738
36.02920.94138.80250.30921.405813.3096-0.23120.1750.124-0.12260.1352-0.0284-0.47050.21450.09610.2515-0.01480.0490.3294-0.01640.297727.342920.889535.0329
411.38551.776111.59920.34911.959612.80660.337-0.69370.06480.1466-0.21170.09090.6372-0.8991-0.12530.2557-0.02330.11530.3423-0.04690.325719.752215.114137.8531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X2 - 29
2X-RAY DIFFRACTION2X30 - 102
3X-RAY DIFFRACTION3X103 - 148
4X-RAY DIFFRACTION4X149 - 184

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