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

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Basic information

Entry
Database: PDB / ID: 7qsu
TitleCrystal structure of homing endonuclease-associated TliVMA intein (C1A, d333-339)
ComponentsV-ATPase
KeywordsHYDROLASE / intein / protein splicing / endonuclease
Function / homologyHoming endonucleases / Endonuclease I-creI / Roll / Alpha Beta
Function and homology information
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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.pdbx_starting_model / _reflns.pdbx_Rmerge_I_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

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Assembly

Deposited unit
A: V-ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6233
Polymers42,2671
Non-polymers3562
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-8 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.570, 43.960, 72.120
Angle α, β, γ (deg.)90.000, 104.620, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein V-ATPase


Mass: 42266.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: SGKAVDGNTLVLTEEFGLVKIKELYEKLDGKGRKTVEGNEEWTELETPVTVYGYRNGRIVGIKATHIYKGISSGMIEIRTRTGRKIKVTPIHKLFTGRVTKDGLALEEVMAMHIKPGDRIAVVKKIDGGEYVKLTTSPDFRKSRKIKVPEVLDEDLAEFLGYLIADGTLKPRTVAIYNNDESLLKRANFLSTKLFGINGKIVQERTVKALLIHSKPLVDFFRKLGIPESKKARNWKVPRELLLSPPSVVKAFINAYIVCDGYYHERKGEIEITTASEEGAYGLSYLLAKLGIYATFRKKQIKGKEYYRIAISGKTNLEKLGIKRETRGYTNIDIVILFDEVVEVKYIPEPQEVYDITTETHNFVGGNMPTLLHN
Source: (gene. exp.) Thermococcus litoralis (archaea) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH 7.5, 70% (v/v) 2-methyl-2,4-pentanediol (MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→37.2 Å / Num. obs: 33640 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.858 / Net I/σ(I): 19.3
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 5361 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
PHENIX1.15.1_3469refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QSS

7qss


Resolution: 1.9→37.2 Å / SU ML: 0.2023 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1656
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2102 1682 5 %
Rwork0.1761 31953 -
obs0.1778 33635 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.34 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 23 114 3052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823000
X-RAY DIFFRACTIONf_angle_d0.8694044
X-RAY DIFFRACTIONf_chiral_restr0.0616460
X-RAY DIFFRACTIONf_plane_restr0.0054503
X-RAY DIFFRACTIONf_dihedral_angle_d8.15662551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.30021360.26582586X-RAY DIFFRACTION99.42
1.95-2.020.27641390.22582651X-RAY DIFFRACTION99.93
2.02-2.090.25781400.21722643X-RAY DIFFRACTION99.96
2.09-2.170.25951390.2042658X-RAY DIFFRACTION100
2.17-2.270.22651390.18972635X-RAY DIFFRACTION100
2.27-2.390.23431400.18032653X-RAY DIFFRACTION100
2.39-2.540.22871390.18622653X-RAY DIFFRACTION100
2.54-2.740.21621420.18712682X-RAY DIFFRACTION100
2.74-3.010.25861400.18532662X-RAY DIFFRACTION99.96
3.01-3.450.22521400.18122671X-RAY DIFFRACTION100
3.45-4.350.21071420.15462699X-RAY DIFFRACTION99.89
4.35-37.20.16411460.16442760X-RAY DIFFRACTION99.73
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)
12.284200293760.2349613504210.802177441083.40904887351-1.882525881953.345344153390.04066951196910.3950495483660.0845798736228-0.338142344985-0.368475793488-0.3855275244420.1955932832410.6561734533220.2115052221760.2429090728740.04240416921970.03098147448280.3168794748520.05474912091860.31975386182146.6874608297-17.990156102249.9340400848
24.504358224020.1561740700862.677627526561.493180172520.2089846341083.17674273464-0.148528465122-0.08133311709090.5007673210560.0401560149765-0.210350038621-0.0123637763571-0.196138521798-0.2296350023410.3997023012740.3279590039970.01196468625680.04213100198510.236541658223-0.006669689932080.26872581299832.0937036831-19.924041259457.7861924164
34.817369857540.7459810777692.372679807052.947115771330.7719354213454.488578294570.06194304572760.12023720883-0.2742698590470.0188381255286-0.1073742627260.1735549157060.440399512003-0.5451169028360.05134182001220.318225459369-0.02983159308170.02036571428220.407199477401-0.1040075745530.31184758069613.4303513862-29.694055698444.6855580976
43.721437280710.7870605807720.4777056064722.84362069678-0.5149698412493.0908217550.11329229534-0.34858100867-0.06970645005110.334019514919-0.09386131247660.01395898406170.141548967973-0.31663337772-0.02931928337630.27810785996-0.0240111934340.01140818938880.262514956819-0.05115185544110.25327576345926.1646980391-26.349029517862.1889547031
53.72000840824-0.08100710050880.6975472642042.9492952861-2.641936803414.413499423860.1013779775530.218433673037-0.0564201824759-0.0606421161214-0.454780006732-0.4395827739970.03330216026040.6087860027690.2577512229840.3257774750950.003580822766640.006745014375220.286466340421-0.0007653844555580.34380236781247.8531783902-22.501184741457.896507595
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 167 )
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 332 )
5X-RAY DIFFRACTION5chain 'A' and (resid 333 through 371 )

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