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- PDB-7cta: Crystal structure of Cx-SAM bound CmoB from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 7cta
TitleCrystal structure of Cx-SAM bound CmoB from Vibrio vulnificus
ComponentstRNA U34 carboxymethyltransferase
KeywordsTRANSFERASE / carboxymethyl transferase / tRNA modification / Cx-SAM
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
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 / tRNA U34 carboxymethyltransferase / tRNA U34 carboxymethyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, J. / Jeong, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural snapshots of CmoB in various states during wobble uridine modification of tRNA.
Authors: Jeong, S. / Kim, J.
History
DepositionAug 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tRNA U34 carboxymethyltransferase
B: tRNA U34 carboxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8656
Polymers76,7882
Non-polymers1,0774
Water1,56787
1
A: tRNA U34 carboxymethyltransferase
B: tRNA U34 carboxymethyltransferase
hetero molecules

A: tRNA U34 carboxymethyltransferase
B: tRNA U34 carboxymethyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,72912
Polymers153,5754
Non-polymers2,1548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)181.962, 50.574, 104.410
Angle α, β, γ (deg.)90.000, 122.700, 90.000
Int Tables number5
Space group name H-MC121
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: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 0 - 325 / Label seq-ID: 1 - 326

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

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Components

#1: Protein tRNA U34 carboxymethyltransferase


Mass: 38393.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus MO6-24/O (bacteria) / Strain: MO6-24/O
Gene: cmoB, CRN46_03385, CRN52_23395, D8T49_20765, D8T54_03695, JS86_05215
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A087JHK9, UniProt: Q8DAP0*PLUS, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Lithium sulfate monohydrate, TRIS hydrochloride pH 8.5, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 17780 / % possible obs: 97.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.075 / Rrim(I) all: 0.148 / Χ2: 0.607 / Net I/σ(I): 3.6 / Num. measured all: 65694
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.953.40.3668510.8890.2240.4310.45494
2.95-33.50.3798540.8960.2270.4430.51196.3
3-3.063.60.3518750.880.2110.4110.54196.5
3.06-3.123.70.3388720.9140.20.3950.51997.4
3.12-3.193.70.2838690.9430.1680.3310.54197.6
3.19-3.273.70.2888920.9440.1690.3350.52198.6
3.27-3.353.70.238920.9440.1370.2690.5299
3.35-3.443.50.2178690.9550.1330.2560.60998
3.44-3.543.60.1968860.9630.1180.230.59797.4
3.54-3.653.90.1559070.9790.090.180.57999.8
3.65-3.783.80.1589000.980.0930.1840.72399.7
3.78-3.943.90.1338940.9790.0780.1550.71798.1
3.94-4.113.80.1048810.9910.0610.120.57398.2
4.11-4.333.80.0968870.9890.0560.1120.63398.1
4.33-4.63.50.0858910.9910.0520.10.62496.8
4.6-4.963.90.0799050.9930.0460.0920.59399.2
4.96-5.463.90.0868970.9920.050.10.60699.2
5.46-6.243.80.0889070.9910.0520.1030.55297.9
6.24-7.863.60.0729090.9920.0430.0850.6297.8
7.86-503.60.0639420.9930.0370.0731.06196.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4qnx

4qnx


Resolution: 2.9→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.51 / SU ML: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 889 5 %RANDOM
Rwork0.1785 ---
obs0.181 16820 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.78 Å2 / Biso mean: 32.002 Å2 / Biso min: 1.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å2-0 Å2-4.08 Å2
2--1.06 Å2-0 Å2
3---1.3 Å2
Refinement stepCycle: final / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 70 87 5480
Biso mean--46.45 18.63 -
Num. residues----656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135548
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175029
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6397557
X-RAY DIFFRACTIONr_angle_other_deg1.1921.57411661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6765654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61121.891312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81315908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8441540
X-RAY DIFFRACTIONr_chiral_restr0.0630.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026161
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021189
Refine LS restraints NCS

Ens-ID: 1 / Number: 10618 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 59 -
Rwork0.274 1205 -
all-1264 -
obs--94.54 %

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