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- PDB-4e2t: Crystal Structures of RadA intein from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 4e2t
TitleCrystal Structures of RadA intein from Pyrococcus horikoshii
ComponentsPho radA intein
KeywordsUNKNOWN FUNCTION / intein / HINT-fold
Function / homology
Function and homology information


intein-mediated protein splicing / ATP-dependent DNA damage sensor activity / DNA recombination / damaged DNA binding / DNA repair / ATP binding
Similarity search - Function
Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA recombination/repair protein RadA / Intein splicing domain / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region ...Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / DNA recombination/repair protein RadA / Intein splicing domain / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / 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 / 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. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DNA repair and recombination protein RadA
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: NMR and Crystal Structures of the Pyrococcus horikoshii RadA Intein Guide a Strategy for Engineering a Highly Efficient and Promiscuous Intein.
Authors: Oeemig, J.S. / Zhou, D. / Kajander, T. / Wlodawer, A. / Iwai, H.
History
DepositionMar 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Sep 13, 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

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Assembly

Deposited unit
A: Pho radA intein
B: Pho radA intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4447
Polymers39,8372
Non-polymers6075
Water2,180121
1
A: Pho radA intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4335
Polymers19,9191
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pho radA intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0112
Polymers19,9191
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.120, 67.370, 82.900
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 Pho radA intein / DNA repair and recombination protein radA


Mass: 19918.551 Da / Num. of mol.: 2 / Mutation: C1A,T173A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: radA, PH0263 / Plasmid: pKRRS15 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: O58001
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 3.0 M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.75→33.7 Å / Num. obs: 33297 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 24.97 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.953 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QLM

2qlm


Resolution: 1.75→33.685 Å / SU ML: 0.34 / σ(F): 2 / Phase error: 22.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 999 3 %
Rwork0.1896 --
obs0.1909 33296 99.34 %
all-33297 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.141 Å2 / ksol: 0.411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5608 Å2-0 Å20 Å2
2---1.807 Å2-0 Å2
3----0.7538 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 39 121 2917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122890
X-RAY DIFFRACTIONf_angle_d1.6453921
X-RAY DIFFRACTIONf_dihedral_angle_d14.711080
X-RAY DIFFRACTIONf_chiral_restr0.124434
X-RAY DIFFRACTIONf_plane_restr0.009495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.84230.32141410.2554566X-RAY DIFFRACTION100
1.8423-1.95770.26121410.22444560X-RAY DIFFRACTION100
1.9577-2.10880.25391420.20254602X-RAY DIFFRACTION100
2.1088-2.3210.22941420.18254598X-RAY DIFFRACTION100
2.321-2.65670.25221430.20164617X-RAY DIFFRACTION100
2.6567-3.34670.25471450.18084667X-RAY DIFFRACTION100
3.3467-33.69120.20421450.17794687X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 12.0467 Å / Origin y: 14.0827 Å / Origin z: 21.4735 Å
111213212223313233
T0.1465 Å20.0014 Å2-0.0328 Å2-0.1291 Å2-0.013 Å2--0.1334 Å2
L0.8513 °20.1501 °2-0.8578 °2-0.5274 °2-0.2418 °2--1.1208 °2
S-0.0085 Å °0.0301 Å °0.0596 Å °0.0241 Å °0.0175 Å °-0.0295 Å °-0.016 Å °0.0114 Å °-0.035 Å °
Refinement TLS groupSelection details: all

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