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- PDB-4qnx: Crystal structure of apo-CmoB -

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Basic information

Entry
Database: PDB / ID: 4qnx
TitleCrystal structure of apo-CmoB
ComponentstRNA (mo5U34)-methyltransferase
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Rossmann Fold
Function / homology
Function and homology information


tRNA wobble uridine modification / transferase activity, transferring alkyl or aryl (other than methyl) groups / Transferases; Transferring alkyl or aryl groups, other than methyl groups / methyltransferase activity / protein-containing complex / identical protein binding
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
tRNA U34 carboxymethyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.619 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: tRNA (mo5U34)-methyltransferase
B: tRNA (mo5U34)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,64218
Polymers74,1052
Non-polymers1,53716
Water1,58588
1
A: tRNA (mo5U34)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7258
Polymers37,0521
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: tRNA (mo5U34)-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,91710
Polymers37,0521
Non-polymers8659
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.885, 185.634, 75.445
Angle α, β, γ (deg.)90.00, 101.88, 90.00
Int Tables number5
Space group name H-MC121

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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) / Strain: K12 / Gene: b1871, cmoB, JW1860, yecP / Plasmid: LIC pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P76291, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.26M ammonium sulfate, and 100mM HEPES/NaOH pH 7.5, 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: Jul 1, 2010
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: 2.63→50 Å / Num. all: 30537 / Num. obs: 30190 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.14
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.619→47.537 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 1530 5.07 %
Rwork0.2003 --
obs0.2028 30170 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.619→47.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5159 0 80 88 5327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095373
X-RAY DIFFRACTIONf_angle_d1.1887321
X-RAY DIFFRACTIONf_dihedral_angle_d14.8961943
X-RAY DIFFRACTIONf_chiral_restr0.049791
X-RAY DIFFRACTIONf_plane_restr0.006926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.619-2.70380.35011400.30262530X-RAY DIFFRACTION96
2.7038-2.80040.3191480.28332630X-RAY DIFFRACTION100
2.8004-2.91250.33311220.23962626X-RAY DIFFRACTION100
2.9125-3.04510.29691540.24032627X-RAY DIFFRACTION100
3.0451-3.20560.29781360.24882624X-RAY DIFFRACTION100
3.2056-3.40640.30261280.21742649X-RAY DIFFRACTION100
3.4064-3.66930.25711370.19322626X-RAY DIFFRACTION99
3.6693-4.03840.24171350.18872589X-RAY DIFFRACTION98
4.0384-4.62230.2361420.16852553X-RAY DIFFRACTION96
4.6223-5.8220.20191450.17552574X-RAY DIFFRACTION97
5.822-47.54510.22361430.18742612X-RAY DIFFRACTION97

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