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- PDB-8kbc: Structure of CmTad1 complexed with cAAA -

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Basic information

Entry
Database: PDB / ID: 8kbc
TitleStructure of CmTad1 complexed with cAAA
Components
  • (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
  • Thoeris anti-defense 1
KeywordsVIRAL PROTEIN
Function / homologynucleotide binding / RNA / Thoeris anti-defense 1
Function and homology information
Biological speciesClostridioides mangenotii LM2 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXiao, Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of CmTad1 complexed with cAAA
Authors: Xiao, Y. / Feng, Y.
History
DepositionAug 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
G: Thoeris anti-defense 1
H: Thoeris anti-defense 1
I: Thoeris anti-defense 1
J: Thoeris anti-defense 1
K: Thoeris anti-defense 1
L: Thoeris anti-defense 1
C: Thoeris anti-defense 1
D: Thoeris anti-defense 1
E: Thoeris anti-defense 1
F: Thoeris anti-defense 1
N: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
O: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
P: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
Q: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,23318
Polymers186,10316
Non-polymers1312
Water00
1
A: Thoeris anti-defense 1
B: Thoeris anti-defense 1
G: Thoeris anti-defense 1
H: Thoeris anti-defense 1
I: Thoeris anti-defense 1
J: Thoeris anti-defense 1
N: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
O: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1179
Polymers93,0518
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26380 Å2
ΔGint-231 kcal/mol
Surface area35430 Å2
MethodPISA
2
K: Thoeris anti-defense 1
L: Thoeris anti-defense 1
C: Thoeris anti-defense 1
D: Thoeris anti-defense 1
E: Thoeris anti-defense 1
F: Thoeris anti-defense 1
P: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
Q: (2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1179
Polymers93,0518
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26600 Å2
ΔGint-228 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.935, 145.731, 150.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Thoeris anti-defense 1 / CmTad1


Mass: 15194.333 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides mangenotii LM2 (bacteria)
Strain: LM2 / Gene: tad1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW61
#2: RNA chain
(2-ACETYL-5-METHYLANILINO)(2,6-DIBROMOPHENYL)ACETAMIDE


Mass: 942.660 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 4.22 Å3/Da / Density % sol: 70.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Ammonium sulfate, 10% v/v 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→44.34 Å / Num. obs: 75093 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.062 / Rrim(I) all: 0.227 / Χ2: 0.95 / Net I/σ(I): 9.4
Reflection shellResolution: 2.81→2.88 Å / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 2.143 / Num. measured all: 74955 / Num. unique obs: 5484 / CC1/2: 0.644 / Rpim(I) all: 0.598 / Rrim(I) all: 2.226 / Χ2: 0.86 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→44.27 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 3778 5.05 %
Rwork0.2264 --
obs0.2285 74745 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12765 0 68 0 12833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713167
X-RAY DIFFRACTIONf_angle_d1.26617791
X-RAY DIFFRACTIONf_dihedral_angle_d21.9891821
X-RAY DIFFRACTIONf_chiral_restr0.0681881
X-RAY DIFFRACTIONf_plane_restr0.0072263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.41831130.34082115X-RAY DIFFRACTION81
2.84-2.880.36681160.33452648X-RAY DIFFRACTION100
2.88-2.920.40951430.34452589X-RAY DIFFRACTION99
2.92-2.960.35811650.29932614X-RAY DIFFRACTION100
2.96-30.34071400.28622584X-RAY DIFFRACTION100
3-3.050.29351600.28242609X-RAY DIFFRACTION100
3.05-3.10.39051300.28942645X-RAY DIFFRACTION100
3.1-3.150.31021330.27582635X-RAY DIFFRACTION100
3.15-3.210.35471160.27652624X-RAY DIFFRACTION100
3.21-3.270.33421440.26532608X-RAY DIFFRACTION100
3.27-3.340.30041430.27562609X-RAY DIFFRACTION100
3.34-3.410.30071580.26482626X-RAY DIFFRACTION100
3.41-3.490.29891600.26232629X-RAY DIFFRACTION100
3.49-3.580.29881400.25052597X-RAY DIFFRACTION100
3.58-3.670.28641410.2412660X-RAY DIFFRACTION100
3.67-3.780.31771320.23282610X-RAY DIFFRACTION99
3.78-3.90.27941250.23092652X-RAY DIFFRACTION99
3.9-4.040.26861300.20972654X-RAY DIFFRACTION99
4.04-4.210.25221280.2072658X-RAY DIFFRACTION99
4.21-4.40.25611350.18612625X-RAY DIFFRACTION99
4.4-4.630.18051690.16992631X-RAY DIFFRACTION100
4.63-4.920.20241580.17222651X-RAY DIFFRACTION100
4.92-5.30.21861180.20012702X-RAY DIFFRACTION100
5.3-5.830.22371340.20672710X-RAY DIFFRACTION100
5.83-6.670.2611300.21412706X-RAY DIFFRACTION100
6.67-8.390.24261730.21212722X-RAY DIFFRACTION100
8.4-44.270.22461440.18592854X-RAY DIFFRACTION100

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