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- PDB-4jc0: Crystal structure of Thermotoga maritima holo RimO in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4jc0
TitleCrystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77
ComponentsRibosomal protein S12 methylthiotransferase RimORibosome
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / three-domained enzyme / alpha-beta N-terminal domain / Semi-TIM barrel Radical-SAM domain / beta barrel C-terminal TRAM domain / ribosomal protein S12
Function / homology
Function and homology information


[ribosomal protein uS12] (aspartate89-C3)-methylthiotransferase / aspartic acid methylthiotransferase activity / protein methylthiotransferase activity / tRNA modification / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Transcription Regulator spoIIAA - #200 / Transcription Regulator spoIIAA - #210 / Methylthiotransferase, N-terminal domain / Ribosomal protein S12 methylthiotransferase RimO / TRAM domain / Methylthiotransferase / Methylthiotransferase, N-terminal / Methylthiotransferase, N-terminal domain superfamily / Uncharacterized protein family UPF0004 / Methylthiotransferase N-terminal domain profile. ...Transcription Regulator spoIIAA - #200 / Transcription Regulator spoIIAA - #210 / Methylthiotransferase, N-terminal domain / Ribosomal protein S12 methylthiotransferase RimO / TRAM domain / Methylthiotransferase / Methylthiotransferase, N-terminal / Methylthiotransferase, N-terminal domain superfamily / Uncharacterized protein family UPF0004 / Methylthiotransferase N-terminal domain profile. / Methylthiotransferase, conserved site / Methylthiotransferase radical SAM domain signature. / TRAM domain / Radical SAM, alpha/beta horseshoe / TRAM domain profile. / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Transcription Regulator spoIIAA / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR PENTA-SULFIDE CONNECTED CLUSTERS / Ribosomal protein uS12 methylthiotransferase RimO
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsForouhar, F. / Hussain, M. / Seetharaman, J. / Fang, Y. / Chen, C.X. / Cunningham, K. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. ...Forouhar, F. / Hussain, M. / Seetharaman, J. / Fang, Y. / Chen, C.X. / Cunningham, K. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases.
Authors: Forouhar, F. / Arragain, S. / Atta, M. / Gambarelli, S. / Mouesca, J.M. / Hussain, M. / Xiao, R. / Kieffer-Jaquinod, S. / Seetharaman, J. / Acton, T.B. / Montelione, G.T. / Mulliez, E. / ...Authors: Forouhar, F. / Arragain, S. / Atta, M. / Gambarelli, S. / Mouesca, J.M. / Hussain, M. / Xiao, R. / Kieffer-Jaquinod, S. / Seetharaman, J. / Acton, T.B. / Montelione, G.T. / Mulliez, E. / Hunt, J.F. / Fontecave, M.
History
DepositionFeb 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 20, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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: Ribosomal protein S12 methylthiotransferase RimO
B: Ribosomal protein S12 methylthiotransferase RimO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4484
Polymers100,7212
Non-polymers1,7272
Water0
1
A: Ribosomal protein S12 methylthiotransferase RimO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2242
Polymers50,3601
Non-polymers8641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosomal protein S12 methylthiotransferase RimO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2242
Polymers50,3601
Non-polymers8641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.721, 86.948, 172.795
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 Ribosomal protein S12 methylthiotransferase RimO / Ribosome / S12 MTTase / S12 methylthiotransferase / Ribosome maturation factor RimO


Mass: 50360.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / Gene: rimO, TM1862, TM_1862 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9X2H6, Transferases
#2: Chemical ChemComp-FS5 / IRON/SULFUR PENTA-SULFIDE CONNECTED CLUSTERS / PENTASULFIDE-LINKED IRON CUBANES


Mass: 863.605 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S13

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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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 10
Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 20 mg/ml, 5 DTT, 10 equivalents FeCl3 and Na2S. Reservoir solution: 100 mM CAPS pH 10.0, 40% PEG 4000, 100 mM Sodium ...Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 20 mg/ml, 5 DTT, 10 equivalents FeCl3 and Na2S. Reservoir solution: 100 mM CAPS pH 10.0, 40% PEG 4000, 100 mM Sodium thiosulfate, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 4, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→41.45 Å / Num. all: 63690 / Num. obs: 14135 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 85.6 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.091 / Net I/σ(I): 13.71
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 2.34 / Rsym value: 0.368 / % possible all: 81.4

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Processing

Software
NameVersionClassification
CNS1.3refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QGQ

2qgq


Resolution: 3.3→41.46 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 91392.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1210 10.3 %RANDOM
Rwork0.245 ---
obs0.245 11747 83.1 %-
all-14135 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.3039 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 101.7 Å2
Baniso -1Baniso -2Baniso -3
1--16.78 Å20 Å20 Å2
2---32.01 Å20 Å2
3---48.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 3.3→41.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 42 0 6850
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.441 175 10.7 %
Rwork0.375 1455 -
obs--70.5 %

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