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- PDB-4o1s: Crystal structure of TvoVMA intein -

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Basic information

Entry
Database: PDB / ID: 4o1s
TitleCrystal structure of TvoVMA intein
ComponentsV-type ATP synthase alpha chain
KeywordsSPLICING
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 / ATP binding
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein splicing domain / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit N-term extension / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
V-type ATP synthase alpha chain
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7008 Å
AuthorsAranko, A.S. / Oeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H.
CitationJournal: Mol Biosyst / Year: 2014
Title: Structure-based engineering and comparison of novel split inteins for protein ligation.
Authors: Aranko, A.S. / Oeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: V-type ATP synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,19310
Polymers37,1182
Non-polymers1,0758
Water2,252125
1
A: V-type ATP synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2046
Polymers18,5591
Non-polymers6455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: V-type ATP synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9894
Polymers18,5591
Non-polymers4303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-7 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.442, 154.442, 48.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein V-type ATP synthase alpha chain / V-ATPase subunit A / Tvo AtpA intein / Tvo VMA intein


Mass: 18559.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea)
Strain: ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1
Gene: atpA, TV0051, TVG0054274 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97CQ0, H+-transporting two-sector ATPase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 4.54 Å3/Da / Density % sol: 72.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES, pH7.0, 25% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2013
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 18676 / Num. obs: 18582 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.119
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.589 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000phasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IN0

2in0


Resolution: 2.7008→45.993 Å / SU ML: 0.42 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 908 5.09 %RANDOM
Rwork0.1803 ---
all0.1828 18582 --
obs0.1828 17824 95.52 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.336 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0459 Å20 Å2-0 Å2
2--2.0459 Å20 Å2
3----4.0917 Å2
Refinement stepCycle: LAST / Resolution: 2.7008→45.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 63 125 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112722
X-RAY DIFFRACTIONf_angle_d1.4513670
X-RAY DIFFRACTIONf_dihedral_angle_d17.281028
X-RAY DIFFRACTIONf_chiral_restr0.085410
X-RAY DIFFRACTIONf_plane_restr0.006459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7008-2.870.38981190.29872225X-RAY DIFFRACTION76
2.87-3.09150.3391730.23752859X-RAY DIFFRACTION99
3.0915-3.40250.25711570.19342913X-RAY DIFFRACTION100
3.4025-3.89470.2031430.15272958X-RAY DIFFRACTION100
3.8947-4.9060.18061630.13432938X-RAY DIFFRACTION99
4.906-45.99970.1991530.19243023X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 38.1485 Å / Origin y: 49.9247 Å / Origin z: 10.9033 Å
111213212223313233
T0.0983 Å20.0457 Å2-0.0153 Å2-0.1361 Å20.0222 Å2--0.1273 Å2
L0.905 °2-0.5295 °2-1.052 °2-0.8208 °20.8253 °2--1.3241 °2
S0.0402 Å °0.0265 Å °0.0045 Å °-0.046 Å °-0.0428 Å °-0.0184 Å °0.0598 Å °-0.0623 Å °0.0282 Å °
Refinement TLS groupSelection details: all

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