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- PDB-2in8: crystal structure of Mtu recA intein, splicing domain -

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Basic information

Entry
Database: PDB / ID: 2in8
Titlecrystal structure of Mtu recA intein, splicing domain
ComponentsEndonuclease PI-MtuI
KeywordsHYDROLASE
Function / homology
Function and homology information


DNA strand invasion / DNA strand exchange activity / UV protection / intein-mediated protein splicing / intron homing / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity ...DNA strand invasion / DNA strand exchange activity / UV protection / intein-mediated protein splicing / intron homing / SOS response / recombinational repair / ATP-dependent DNA damage sensor activity / ATP-dependent activity, acting on DNA / DNA endonuclease activity / manganese ion binding / single-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / response to antibiotic / DNA repair / DNA damage response / magnesium ion binding / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / LAGLIDADG-like domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / LAGLIDADG-like domain / DNA recombination/repair protein RecA, conserved site / DNA recombination and repair protein RecA, C-terminal / : / RecA C-terminal domain / recA signature. / DNA recombination and repair protein RecA / : / recA bacterial DNA recombination protein / Intein splicing 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 / 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 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / Beta Complex / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Protein RecA / Protein RecA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVan Roey, P.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystallographic and mutational studies of Mycobacterium tuberculosis recA mini-inteins suggest a pivotal role for a highly conserved aspartate residue.
Authors: Van Roey, P. / Pereira, B. / Li, Z. / Hiraga, K. / Belfort, M. / Derbyshire, V.
History
DepositionOct 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 30, 2023Group: 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: Endonuclease PI-MtuI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4042
Polymers15,3071
Non-polymers961
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.870, 49.270, 64.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endonuclease PI-MtuI


Mass: 15307.439 Da / Num. of mol.: 1 / Fragment: splicing domain
Mutation: delta 103-403, D24G, V67L, Q95V, P96R, R97D, R98V, F99E, D100T, F102E, D422G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: recA / Production host: Escherichia coli (E. coli) / Strain (production host): JM101
References: UniProt: P0A5U4, UniProt: P9WHJ3*PLUS, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.91 Å3/Da / Density % sol: 35.67 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 65% ammonium sulfate 100 mM Tris.HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2006 / Details: osmic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 13488 / Num. obs: 13488 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.9
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.1 / % possible all: 92.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data collection
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2IMZ

2imz


Resolution: 1.7→29.52 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 945804.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1322 9.9 %RANDOM
Rwork0.252 ---
obs0.252 13338 99 %-
all-13338 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.6805 Å2 / ksol: 0.368209 e/Å3
Displacement parametersBiso mean: 28 Å2
Baniso -1Baniso -2Baniso -3
1--7.82 Å20 Å20 Å2
2--17.76 Å20 Å2
3----9.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 5 114 1199
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.499 223 10.4 %
Rwork0.519 1928 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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