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- PDB-1ir6: Crystal structure of exonuclease RecJ bound to manganese -

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Basic information

Entry
Database: PDB / ID: 1ir6
TitleCrystal structure of exonuclease RecJ bound to manganese
Componentsexonuclease RecJ
KeywordsHYDROLASE / manganese / DNA repair / DNA recombination / nuclease / single-stranded DNA / two domains interconnected by alpha-helix / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


exonuclease activity / nucleic acid binding / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
Single-stranded-DNA-specific exonuclease RecJ C-terminal domain / inorganic pyrophosphatase (n-terminal core) - #30 / RecJ, OB domain / RecJ OB domain / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily ...Single-stranded-DNA-specific exonuclease RecJ C-terminal domain / inorganic pyrophosphatase (n-terminal core) - #30 / RecJ, OB domain / RecJ OB domain / Diaminopimelate Epimerase; Chain A, domain 1 - #30 / : / inorganic pyrophosphatase (n-terminal core) / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Single-stranded-DNA-specific exonuclease RecJ / Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / single-wavelength anomalous dispersion / Resolution: 2.9 Å
AuthorsYamagata, A. / Kakuta, Y. / Masui, R. / Fukuyama, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The crystal structure of exonuclease RecJ bound to Mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.
Authors: Yamagata, A. / Kakuta, Y. / Masui, R. / Fukuyama, K.
#1: Journal: Nucleic Acids Res. / Year: 2001
Title: Overexpression, purification and characterization of RecJ protein from Thermus thermophilus HB8 and its core domain
Authors: Yamagata, A. / Masui, R. / Kakuta, Y. / Kuramitsu, S. / Fukuyama, K.
History
DepositionSep 11, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THERE ARE 2 DIFFERENCES BETWEEN THE DEPOSITORS DATA AND THE GENETIC SEQUENCE(S) IN THE ...SEQUENCE THERE ARE 2 DIFFERENCES BETWEEN THE DEPOSITORS DATA AND THE GENETIC SEQUENCE(S) IN THE 14595119 ENTRY. THERE IS NO QUESTION FROM THE ELECTRON DENSITY THAT these residues are not database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: exonuclease RecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9522
Polymers45,8971
Non-polymers551
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.600, 141.600, 141.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein exonuclease RecJ / single-stranded DNA specific exonuclease RecJ


Mass: 45896.973 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / References: UniProt: Q93R48, UniProt: Q5SJ47*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn

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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: 5.15 Å3/Da / Density % sol: 76.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: ammonium sulfate, sodium/potassium tartrate, sodium citrate, glycerol, manganese chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.0 Mammonium sulfate1reservoir
20.2 Msodium potassium tartrate1reservoir
350 mMsodium citrate1reservoir
410 %glycerol1reservoirpH5.8
510 mg/mlprotein1drop
620 mMTris-HCl1drop
7100 mM1dropNaCl
80.1 mMEDTA1drop
910 %glycerol1droppH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2001
RadiationMonochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→57.808 Å / Num. all: 21198 / Num. obs: 21198 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.049
Reflection shellResolution: 2.9→3.08 Å / Rsym value: 0.279 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 60 Å / Num. measured all: 584147 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.279

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: single-wavelength anomalous dispersion
Resolution: 2.9→19.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 418520.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1008 4.9 %RANDOM
Rwork0.228 ---
all0.228 20777 --
obs0.228 20777 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.0741 Å2 / ksol: 0.326039 e/Å3
Displacement parametersBiso mean: 62.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 1 0 2920
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 147 4.5 %
Rwork0.362 3145 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.228 / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
LS refinement shell
*PLUS
Rfactor Rfree: 0.39 / Rfactor Rwork: 0.362 / Rfactor obs: 0.362

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