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- PDB-7ct9: Crystal structure of SAH bound CmoB from Vibrio Vulnificus -

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Basic information

Entry
Database: PDB / ID: 7ct9
TitleCrystal structure of SAH bound CmoB from Vibrio Vulnificus
ComponentstRNA U34 carboxymethyltransferase
KeywordsTRANSFERASE / carboxymethyl transferase / tRNA modification / SAH / S-adenosyl homocysteine
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
MALONATE ION / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / tRNA U34 carboxymethyltransferase / tRNA U34 carboxymethyltransferase
Similarity search - Component
Biological speciesVibrio vulnificus MO6-24/O (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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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)77,9508
Polymers76,7882
Non-polymers1,1636
Water6,954386
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)155,90116
Polymers153,5754
Non-polymers2,32612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8550 Å2
ΔGint-61 kcal/mol
Surface area49260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.535, 50.462, 104.791
Angle α, β, γ (deg.)90.000, 122.970, 90.000
Int Tables number5
Space group name H-MC121
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: SAH / End label comp-ID: SAH / Refine code: _ / Auth seq-ID: 0 - 401 / Label seq-ID: 1

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

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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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium malonate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 36969 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.069 / Rrim(I) all: 0.138 / Χ2: 1.636 / Net I/σ(I): 6.8 / Num. measured all: 147619
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.90.82818180.7010.4780.9591.46399.9
2.34-2.383.90.62817970.730.3620.7271.54999.9
2.38-2.433.90.6118410.7760.3490.7051.49999.9
2.43-2.4840.57118460.8310.3250.6591.524100
2.48-2.5340.52418410.8460.2990.6061.59599.9
2.53-2.5940.44318450.8790.2530.5111.57299.9
2.59-2.6640.42418420.8850.2410.4891.59699.9
2.66-2.7340.34618210.9210.1980.41.6599.9
2.73-2.814.10.31318380.9390.1780.3611.588100
2.81-2.940.25818420.9510.1480.2991.59899.9
2.9-34.10.20418570.9740.1150.2351.64499.9
3-3.124.10.16818110.9740.0950.1941.68999.9
3.12-3.264.10.13918530.9850.0790.161.63899.9
3.26-3.444.10.10718460.9890.0610.1241.64999.9
3.44-3.654.10.08518780.9930.0480.0981.75199.8
3.65-3.9340.07118440.9940.0410.0821.96399.9
3.93-4.3340.05618540.9970.0320.0651.62399.7
4.33-4.9540.05318680.9960.0310.0611.75699.8
4.95-6.2440.05418900.9960.0310.0631.57799.9
6.24-503.70.04819370.9950.030.0571.77699.1

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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: 2.3→30.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.749 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 1784 5 %RANDOM
Rwork0.1718 ---
obs0.1746 34208 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.89 Å2 / Biso mean: 25.242 Å2 / Biso min: 10.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å2-0 Å2-2 Å2
2--1.09 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 2.3→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5291 0 76 386 5753
Biso mean--30.77 29 -
Num. residues----656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175008
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6397537
X-RAY DIFFRACTIONr_angle_other_deg1.3091.57311602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5785656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66221.836305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30715894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5351539
X-RAY DIFFRACTIONr_chiral_restr0.0770.2689
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021189
Refine LS restraints NCS

Ens-ID: 1 / Number: 11046 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 116 -
Rwork0.278 2506 -
all-2622 -
obs--99.92 %

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