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- PDB-7ct8: Crystal structure of apo CmoB from Vibrio Vulnificus -

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Basic information

Entry
Database: PDB / ID: 7ct8
TitleCrystal structure of apo CmoB from Vibrio Vulnificus
ComponentstRNA U34 carboxymethyltransferase
KeywordsTRANSFERASE / carboxymethyl transferase / tRNA modification
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
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 / tRNA U34 carboxymethyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,7882
Polymers76,7882
Non-polymers00
Water4,324240
1
A: tRNA U34 carboxymethyltransferase
B: tRNA U34 carboxymethyltransferase

A: tRNA U34 carboxymethyltransferase
B: tRNA U34 carboxymethyltransferase


Theoretical massNumber of molelcules
Total (without water)153,5754
Polymers153,5754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6430 Å2
ΔGint-34 kcal/mol
Surface area56000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.121, 89.896, 88.711
Angle α, β, γ (deg.)90.000, 114.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-449-

HOH

21B-426-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / 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: _ / Auth seq-ID: 0 - 328 / Label seq-ID: 1 - 329

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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate trihydrate, Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 56139 / % possible obs: 99 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.046 / Rrim(I) all: 0.119 / Χ2: 0.949 / Net I/σ(I): 5 / Num. measured all: 370749
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.11.05427690.7530.4461.1480.51598.7
2.14-2.186.10.84627760.8730.3580.9210.52298.8
2.18-2.226.30.77727980.890.3270.8450.51898.9
2.22-2.266.30.6828270.9330.2880.740.69499.1
2.26-2.316.40.66227680.9260.2770.7190.55399.3
2.31-2.376.40.58228080.9280.2440.6320.54699.4
2.37-2.426.40.49928100.9490.210.5430.53799.1
2.42-2.4960.45527910.9590.2010.4990.52897.9
2.49-2.566.90.3227930.980.130.3460.54499.5
2.56-2.6570.28928070.9790.1160.3120.61699.4
2.65-2.7470.25527870.9850.1030.2750.71299.4
2.74-2.8570.19228260.9910.0780.2070.68899.4
2.85-2.986.90.1628080.9920.0650.1730.74599.6
2.98-3.146.70.12828360.9920.0530.1390.87499.1
3.14-3.336.40.10727760.9940.0450.1171.04198.2
3.33-3.597.10.0928290.9960.0360.0971.37599.5
3.59-3.9570.0827960.9960.0320.0861.70699.4
3.95-4.526.70.06928610.9970.0290.0751.87899
4.52-5.76.70.06527920.9960.0270.0711.89498.3
5.7-506.70.06228810.9970.0260.0682.18698.5

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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: 2.1→48.42 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 6.953 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.147
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2133 2833 5 %RANDOM
Rwork0.1794 ---
obs0.1811 53295 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.62 Å2 / Biso mean: 42.607 Å2 / Biso min: 20.13 Å2
Baniso -1Baniso -2Baniso -3
1-4.18 Å2-0 Å2-3.93 Å2
2---0.01 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 2.1→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 0 240 5490
Biso mean---42.23 -
Num. residues----654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135433
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174933
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.6367404
X-RAY DIFFRACTIONr_angle_other_deg1.291.57311428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.825657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88122.121297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92115882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4251535
X-RAY DIFFRACTIONr_chiral_restr0.0720.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026085
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021168
Refine LS restraints NCS

Ens-ID: 1 / Number: 9991 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.151 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.336 168 -
Rwork0.319 3659 -
obs--92.04 %

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