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- PDB-8ka1: Crystal structure of Vibrio vulnificus RID-dependent transforming... -

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Basic information

Entry
Database: PDB / ID: 8ka1
TitleCrystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin
Components
  • Calmodulin-2
  • RDTND-RID CBD
KeywordsTOXIN / MARTX toxin / RDTND-RID / NADase / CaM
Function / homology
Function and homology information


negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex ...negative regulation of calcium ion transmembrane transporter activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / negative regulation of calcium ion export across plasma membrane / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / spindle pole / response to calcium ion / G2/M transition of mitotic cell cycle / calcium-dependent protein binding / myelin sheath / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Serine aminopeptidase, S33 / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serine aminopeptidase, S33 ...RtxA toxin / RtxA repeat / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / Serine aminopeptidase, S33 / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serine aminopeptidase, S33 / Serralysin-like metalloprotease, C-terminal / EF-hand domain pair / Galactose-binding-like domain superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
RTX toxin / Calmodulin-2
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsLee, Y. / Choi, S. / Hwang, J. / Kim, M.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Other governmentthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM1382312) Korea, Republic Of
Other governmentthe Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM2112335) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of Vibrio vulnificus RID-dependent transforming NADase domain (RDTND)/calmodulin-binding domain of Rho inactivation domain (RID-CBD) complexed with Ca2+-free calmodulin
Authors: Lee, Y. / Choi, S. / Hwang, J. / Kim, M.H.
History
DepositionAug 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 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: RDTND-RID CBD
B: Calmodulin-2
C: RDTND-RID CBD
D: Calmodulin-2
E: RDTND-RID CBD
F: Calmodulin-2
G: RDTND-RID CBD
H: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,17811
Polymers259,1058
Non-polymers733
Water32418
1
A: RDTND-RID CBD
B: Calmodulin-2


Theoretical massNumber of molelcules
Total (without water)64,7762
Polymers64,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-22 kcal/mol
Surface area26840 Å2
MethodPISA
2
C: RDTND-RID CBD
D: Calmodulin-2


Theoretical massNumber of molelcules
Total (without water)64,7762
Polymers64,7762
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-25 kcal/mol
Surface area24970 Å2
MethodPISA
3
E: RDTND-RID CBD
F: Calmodulin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8495
Polymers64,7762
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-52 kcal/mol
Surface area26990 Å2
MethodPISA
4
G: RDTND-RID CBD
H: Calmodulin-2


Theoretical massNumber of molelcules
Total (without water)64,7762
Polymers64,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-24 kcal/mol
Surface area25410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.032, 88.081, 136.954
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RDTND-RID CBD / MARTX


Mass: 47327.617 Da / Num. of mol.: 4 / Fragment: MARTX toxin DUF1-RIDcbd region
Source method: isolated from a genetically manipulated source
Details: NCBI accession ID: WP_015728045.1 / Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN52_02910 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2S3R7M0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein
Calmodulin-2


Mass: 17448.643 Da / Num. of mol.: 4 / Mutation: E124Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM2, CAM2, CAMB / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP24
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) PEG 3350, 0.1 M HEPES-NaOH (pH 7.5), 0.28 M MgCl2, and 6 mM MnCl2

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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: Mar 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.82→50 Å / Num. obs: 55183 / % possible obs: 98.1 % / Redundancy: 4.7 % / CC1/2: 0.988 / Net I/σ(I): 5.3
Reflection shellResolution: 2.82→2.87 Å / Num. unique obs: 2330 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8K9Z

8k9z


Resolution: 2.82→49.53 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.836 / Cross valid method: THROUGHOUT / ESU R Free: 0.583 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3415 2678 4.9 %RANDOM
Rwork0.27143 ---
obs0.275 51961 89.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.533 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å2-0 Å2-0.16 Å2
2---0.68 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 2.82→49.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17045 0 3 18 17066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01217360
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616120
X-RAY DIFFRACTIONr_angle_refined_deg1.0441.65223439
X-RAY DIFFRACTIONr_angle_other_deg0.7761.58237141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48652124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.1085110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.511102885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.22554
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0220782
X-RAY DIFFRACTIONr_gen_planes_other0.0080.024006
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1685.3748532
X-RAY DIFFRACTIONr_mcbond_other3.1685.3748532
X-RAY DIFFRACTIONr_mcangle_it5.3699.6910644
X-RAY DIFFRACTIONr_mcangle_other5.3699.69110645
X-RAY DIFFRACTIONr_scbond_it3.3545.6028828
X-RAY DIFFRACTIONr_scbond_other3.3545.6038829
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.56710.17812796
X-RAY DIFFRACTIONr_long_range_B_refined11.38464.9769250
X-RAY DIFFRACTIONr_long_range_B_other11.38464.9769249
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 93 -
Rwork0.348 1936 -
obs--45.71 %

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