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- PDB-7qss: Crystal structure of homing endonuclease-associated TliVMA intein... -

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Basic information

Entry
Database: PDB / ID: 7qss
TitleCrystal structure of homing endonuclease-associated TliVMA intein (C1A)
ComponentsV-type ATP synthase alpha chain
KeywordsHYDROLASE / intein / protein splicing / endonuclease
Function / homology
Function and homology information


intein-mediated protein splicing / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / endonuclease activity / ATP binding
Similarity search - Function
LAGLIDADG-like domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / 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 ...LAGLIDADG-like domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Homing endonuclease, LAGLIDADG / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FORMIC ACID / V-type ATP synthase alpha chain
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBeyer, H.M. / Iwai, H.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Academy of Finland137995, 277335 Denmark
Novo Nordisk FoundationNNF17OC0025402, NNF17OC0027550 Denmark
CitationJournal: Front Mol Biosci / Year: 2022
Title: Structural Basis for the Propagation of Homing Endonuclease-Associated Inteins.
Authors: Beyer, H.M. / Iwai, H.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Data collection / Refinement description / Structure summary
Category: refine / reflns / struct
Item: _refine.ls_percent_reflns_obs / _refine.pdbx_starting_model ..._refine.ls_percent_reflns_obs / _refine.pdbx_starting_model / _reflns.pdbx_Rmerge_I_obs / _reflns.percent_possible_obs / _struct.title
Revision 1.2Apr 13, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: V-type ATP synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9822
Polymers48,9361
Non-polymers461
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.800, 96.180, 96.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein V-type ATP synthase alpha chain / V-ATPase subunit A


Mass: 48936.395 Da / Num. of mol.: 1 / Mutation: C1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis (archaea) / Gene: atpA, OCC_09254 / Production host: Escherichia coli (E. coli)
References: UniProt: H3ZKG9, H+-transporting two-sector ATPase
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM magnesium formate and 15% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.56→27.96 Å / Num. obs: 65400 / % possible obs: 99.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 21.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.569 / Net I/σ(I): 13.32
Reflection shellResolution: 1.56→1.65 Å / Num. unique obs: 10414 / CC1/2: 0.807

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QST

7qst


Resolution: 1.56→27.96 Å / SU ML: 0.1829 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 3270 5 %
Rwork0.1812 62124 -
obs0.1826 65394 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.57 Å2
Refinement stepCycle: LAST / Resolution: 1.56→27.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 3 433 3886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033567
X-RAY DIFFRACTIONf_angle_d1.13884818
X-RAY DIFFRACTIONf_chiral_restr0.0722543
X-RAY DIFFRACTIONf_plane_restr0.007611
X-RAY DIFFRACTIONf_dihedral_angle_d17.2003493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.580.2921390.27252656X-RAY DIFFRACTION99.08
1.58-1.610.28631400.27352661X-RAY DIFFRACTION99.47
1.61-1.630.33661410.25932671X-RAY DIFFRACTION99.54
1.63-1.660.27361410.24382668X-RAY DIFFRACTION100
1.66-1.690.27221410.2412688X-RAY DIFFRACTION100
1.69-1.720.22941410.22672669X-RAY DIFFRACTION99.89
1.72-1.760.26891400.22222674X-RAY DIFFRACTION99.96
1.76-1.80.21651420.20222685X-RAY DIFFRACTION100
1.8-1.840.24291400.19772671X-RAY DIFFRACTION99.93
1.84-1.890.23531430.19652708X-RAY DIFFRACTION99.86
1.89-1.940.22041410.21662677X-RAY DIFFRACTION99.61
1.94-1.990.23941400.19792675X-RAY DIFFRACTION99.68
1.99-2.060.20341420.18662681X-RAY DIFFRACTION99.68
2.06-2.130.22521420.1832699X-RAY DIFFRACTION99.16
2.13-2.220.23161410.1852684X-RAY DIFFRACTION99.09
2.22-2.320.23631400.19012662X-RAY DIFFRACTION98.77
2.32-2.440.21321430.18182717X-RAY DIFFRACTION99.97
2.44-2.590.21071430.18242713X-RAY DIFFRACTION99.86
2.59-2.790.21071430.18712728X-RAY DIFFRACTION99.76
2.79-3.070.22731450.17942740X-RAY DIFFRACTION99.76
3.07-3.520.19431440.16282747X-RAY DIFFRACTION99.55
3.52-4.430.18361450.15282752X-RAY DIFFRACTION98.44
4.43-27.960.16621530.16242898X-RAY DIFFRACTION99.28
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2260152577280.083871165481-0.1247118639271.78518724362-0.9634561196931.285258593660.00903661787855-0.0270364064328-0.064318257406-0.088222102727-0.02053769975740.09916633284170.181378265-0.01723061715370.00996433655560.1934739548680.021308179807-0.003584157530890.164663790609-0.009355718613410.20783065743315.0050227766-0.61942059779416.2529691613
21.14371530254-0.385111457707-1.340816018221.015260257141.149973822653.356605845630.0194727068535-0.195517057382-0.00614591755930.128387657198-0.117757911380.114428135123-0.0866359408956-0.02608854274060.09561624384660.212165713625-0.0315533958696-0.0002820768122440.2132236666840.01962153060030.1970197993726.051846900223.387076814835.9350029508
31.97144641048-0.151109547194-0.7883474002711.150497435660.4296141653422.239078244150.0548472579846-0.1644044795810.01150447764520.188059888714-0.000471687609193-0.0578873997224-0.07248934712520.1643403089810.02299572024980.133103858668-0.012533108931-0.002155834682060.132046728005-0.004551953303470.12795095905615.094785132121.737402412326.4253208223
40.376041973918-0.08728450271670.08509419731350.554728231889-0.540651609691.6535573632-0.02214740472040.01815085525570.0199883601769-0.0247512272104-0.0176273635205-0.0575085057779-0.07625317406450.1024474708070.04077053928590.139835502708-0.0007551380224470.008300950315430.164507170969-0.006196177466550.18284755182218.94111160517.068718746.14409200304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 220 )
3X-RAY DIFFRACTION3chain 'A' and (resid 221 through 287 )
4X-RAY DIFFRACTION4chain 'A' and (resid 288 through 429 )

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