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- PDB-4kb4: Crystal structure of ribosome recycling factor mutant R31A from M... -

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Basic information

Entry
Database: PDB / ID: 4kb4
TitleCrystal structure of ribosome recycling factor mutant R31A from Mycobacterium tuberculosis
ComponentsRibosome-recycling factor
KeywordsTRANSLATION / Ribosome recycling / 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: 2.25 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 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 / pdbx_struct_conn_angle / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Ribosome-recycling factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0003
Polymers20,7761
Non-polymers2252
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.200, 40.450, 68.540
Angle α, β, γ (deg.)90.00, 118.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 20775.547 Da / Num. of mol.: 1 / Mutation: R31A
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.: 84 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 298 K / Method: under oil in microbatch plates / pH: 7.8
Details: 6% Polyethylene glycol 4000, 20mM Tris-HCl, 0.6mM cadmium acetate, 5% polyethylene glycol 400, pH 7.8, Under oil in microbatch plates, temperature 298KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.514 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.25→60.3 Å / Num. obs: 11114 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 12.5 / Num. unique all: 11114 / % possible all: 100

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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: 2.25→46.24 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.282 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26385 531 4.8 %RANDOM
Rwork0.21574 ---
obs0.21812 10582 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0.33 Å2
2---1.6 Å20 Å2
3---1.18 Å2
Refine analyzeLuzzati coordinate error free: 0.228 Å
Refinement stepCycle: LAST / Resolution: 2.25→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 2 84 1516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191445
X-RAY DIFFRACTIONr_bond_other_d0.0020.021442
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9731948
X-RAY DIFFRACTIONr_angle_other_deg0.95433312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6555183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1824.28670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.7915273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6221515
X-RAY DIFFRACTIONr_chiral_restr0.090.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 31 -
Rwork0.258 752 -
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)
115.38491.418-16.77223.0752-3.06123.32210.0901-0.03440.14930.02480.02260.0592-0.3862-0.2694-0.11270.1004-0.0036-0.00910.0283-0.0110.055316.5664-9.15497.6014
27.2705-5.15930.76918.1242-1.92196.2649-0.7791-1.4070.09441.32680.8496-0.8305-0.06810.5314-0.07050.36280.157-0.09190.6198-0.06230.1851-8.3635-5.690519.2679
37.43460.5268-9.20481.7745-1.622318.3772-0.3211-0.0135-0.2438-0.01820.03270.2010.5655-0.72750.28830.1412-0.01550.04090.0847-0.01580.079214.0434-18.94757.972
49.2466-1.0058-10.3462.61960.559217.9880.0619-0.49540.17370.05370.1033-0.1094-0.04850.2326-0.16520.0623-0.0059-0.01590.07230.00170.019322.9838-15.901211.1686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 29
2X-RAY DIFFRACTION2A30 - 102
3X-RAY DIFFRACTION3A103 - 148
4X-RAY DIFFRACTION4A149 - 185

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