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- PDB-1jva: CRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N ... -

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Basic information

Entry
Database: PDB / ID: 1jva
TitleCRYSTAL STRUCTURE OF THE VMA1-DERIVED ENDONUCLEASE BEARING THE N AND C EXTEIN PROPEPTIDES
ComponentsVMA1-DERIVED HOMING ENDONUCLEASE X10SSS
KeywordsHYDROLASE / PROTEIN-SPLICING / VMA1-DERIVED ENDONUCLEASE / INTEIN / THIAZOLIDINE INTERMEDIATE / VDE
Function / homology
Function and homology information


Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / endosomal lumen acidification / proton-transporting V-type ATPase complex / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / intron homing / protein metabolic process / intein-mediated protein splicing / fungal-type vacuole membrane / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / Hydrolases; Acting on ester bonds / Golgi membrane / mRNA binding / DNA binding / ATP binding
Similarity search - Function
Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein / Homing endonucleases / Endonuclease I-creI / Intein DOD homing endonuclease ...Homing endonuclease PI-Sce / Homing endonuclease / Hom-end-associated Hint / Hom_end-associated Hint / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein / Homing endonucleases / Endonuclease I-creI / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Beta Complex / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
V-type proton ATPase catalytic subunit A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMizutani, R. / Satow, Y.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Protein-splicing reaction via a thiazolidine intermediate: crystal structure of the VMA1-derived endonuclease bearing the N and C-terminal propeptides.
Authors: Mizutani, R. / Nogami, S. / Kawasaki, M. / Ohya, Y. / Anraku, Y. / Satow, Y.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae
Authors: Hirata, R. / Ohsumi, Y. / Nakano, A. / Kawasaki, H. / Suzuki, K. / Anraku, Y.
History
DepositionAug 29, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: VMA1-DERIVED HOMING ENDONUCLEASE X10SSS
B: VMA1-DERIVED HOMING ENDONUCLEASE X10SSS


Theoretical massNumber of molelcules
Total (without water)106,3002
Polymers106,3002
Non-polymers00
Water3,693205
1
A: VMA1-DERIVED HOMING ENDONUCLEASE X10SSS


Theoretical massNumber of molelcules
Total (without water)53,1501
Polymers53,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VMA1-DERIVED HOMING ENDONUCLEASE X10SSS


Theoretical massNumber of molelcules
Total (without water)53,1501
Polymers53,1501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.178, 68.846, 58.524
Angle α, β, γ (deg.)103.10, 98.79, 78.98
Int Tables number1
Space group name H-MP1
DetailsVDE exists as a monomer in solution.

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Components

#1: Protein VMA1-DERIVED HOMING ENDONUCLEASE X10SSS / X10SSS VDE


Mass: 53150.145 Da / Num. of mol.: 2 / Fragment: RESIDUES 274-747 / Mutation: C284S/H362N/N737S/C738S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VMA1 / Plasmid: pET-17b-VDE-X10SSS / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17255, EC: 3.6.1.34
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.39 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG6000, BisTrisHCl, mercaptoethanol, magnesium chloride, cadmium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117 %(w/v)PEG60001drop
20.1 MBis-Tris-HCl1reservoirpH6.2
310 mM2-mercaptoethanol1reservoir
410 mM1reservoirMgCl2
51 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 0.7 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2000
Details: double crystal monochromator and bent-cylinder mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 57103 / Num. obs: 51056 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Redundancy: 2.39 % / Biso Wilson estimate: 20.12 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 30.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.63 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 2.63 / Num. unique all: 5699 / % possible all: 70.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 122186 / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 70.9 % / Num. unique obs: 4038 / Rmerge(I) obs: 0.155

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VDE

1vde


Resolution: 2.1→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2549 4.5 %RANDOM
Rwork0.198 ---
all0.2 57103 --
obs0.2 51056 89.4 %-
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.493 Å2-4.034 Å25.198 Å2
2--2.688 Å24.241 Å2
3----3.181 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.175 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6755 0 0 205 6960
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2996 182 4.9 %
Rwork0.2474 3749 -
obs-4038 70.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor all: 0.2 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.2996 / Rfactor Rwork: 0.2474

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