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- PDB-4qnv: Crystal structure of Cx-SAM bound CmoB from E. coli in P6122 -

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Basic information

Entry
Database: PDB / ID: 4qnv
TitleCrystal structure of Cx-SAM bound CmoB from E. coli in P6122
ComponentstRNA (mo5U34)-methyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Rossmann fold / carboxymethyl transferase
Function / homology
Function and homology information


tRNA wobble uridine modification / Transferases; Transferring alkyl or aryl groups, other than methyl groups / transferase activity, transferring alkyl or aryl (other than methyl) groups / S-adenosylmethionine-dependent methyltransferase activity
Similarity search - Function
tRNA U34 carboxymethyltransferase / tRNA (Mo5U34)-methyltransferase-like / Protein of unknown function (DUF1698) / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Chem-GEK / PHOSPHATE ION / tRNA U34 carboxymethyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsKim, J. / Toro, R. / Bhosle, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.
Authors: Kim, J. / Xiao, H. / Koh, J. / Wang, Y. / Bonanno, J.B. / Thomas, K. / Babbitt, P.C. / Brown, S. / Lee, Y.S. / Almo, S.C.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ncs_dom_lim / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: tRNA (mo5U34)-methyltransferase
B: tRNA (mo5U34)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1806
Polymers74,1052
Non-polymers1,0754
Water72140
1
A: tRNA (mo5U34)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5903
Polymers37,0521
Non-polymers5372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: tRNA (mo5U34)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5903
Polymers37,0521
Non-polymers5372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.134, 82.134, 432.516
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 1 - 323 / Label seq-ID: 1 - 323

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein tRNA (mo5U34)-methyltransferase


Mass: 37052.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cmoB, Ecok1_17280, APECO1_921 / Plasmid: LIC pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: A1AC32, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GEK / (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio] -2-ammoniobutanoate / CARBOXY-S-ADENOSYLMETHIONINE


Mass: 442.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H22N6O7S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES:NaOH pH 7.5, 0.2M MgCl2, 30% (v/v) PEG400, 10mM TCEP:HCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 3, 2012
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. all: 26963 / Num. obs: 26722 / % possible obs: 99.2 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 15.5
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→43.08 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.875 / SU B: 11.597 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.671 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26947 1337 5 %RANDOM
Rwork0.21836 ---
obs0.22086 25243 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.595 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.2 Å20 Å2
2--0.2 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.64→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 70 40 5295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195392
X-RAY DIFFRACTIONr_bond_other_d0.0040.025132
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9687337
X-RAY DIFFRACTIONr_angle_other_deg0.9253.00411786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4335638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04523.586251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94915905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4731540
X-RAY DIFFRACTIONr_chiral_restr0.080.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215997
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021259
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6784.6342570
X-RAY DIFFRACTIONr_mcbond_other4.6784.6342570
X-RAY DIFFRACTIONr_mcangle_it6.7316.9493202
X-RAY DIFFRACTIONr_mcangle_other6.736.9493203
X-RAY DIFFRACTIONr_scbond_it4.9365.0622822
X-RAY DIFFRACTIONr_scbond_other4.9365.0612823
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1267.4254136
X-RAY DIFFRACTIONr_long_range_B_refined9.23837.6456130
X-RAY DIFFRACTIONr_long_range_B_other9.23837.656126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 20116 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.64→2.706 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 89 -
Rwork0.319 1806 -
obs--99.79 %

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