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- PDB-2zxr: Crystal structure of RecJ in complex with Mg2+ from Thermus therm... -

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Basic information

Entry
Database: PDB / ID: 2zxr
TitleCrystal structure of RecJ in complex with Mg2+ from Thermus thermophilus HB8
ComponentsSingle-stranded DNA specific exonuclease RecJ
KeywordsHYDROLASE / nuclease / single-stranded DNA / DNA repair / Exonuclease
Function / homology
Function and homology information


exonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #460 / Rossmann fold - #12810 / 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 ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #460 / Rossmann fold - #12810 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Alpha-Beta Complex / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Single-stranded-DNA-specific exonuclease RecJ
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWakamatsu, T. / Kitamura, Y. / Nakagawa, N. / Masui, R. / Kuramitsu, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of RecJ exonuclease defines its specificity for single-stranded DNA
Authors: Wakamatsu, T. / Kitamura, Y. / Kotera, Y. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJan 5, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Single-stranded DNA specific exonuclease RecJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9852
Polymers72,9601
Non-polymers241
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.357, 83.357, 251.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Single-stranded DNA specific exonuclease RecJ


Mass: 72960.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: recj, TTHA1167 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS
References: UniProt: Q5SJ47, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ADA, 6% PEG4000, 1% 2-propanol. The crystal was soaked in cryoprotecting solution containg 20% glycerol and 10mM magnesium sulfate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 18, 2008
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 48684 / Num. obs: 48684 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 17.2 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 47.2
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.3 / Num. unique all: 837996 / % possible all: 86

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZXO

2zxo


Resolution: 2.15→43.01 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 4815 -random
Rwork0.235 ---
all-47494 --
obs-47494 96.5 %-
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---1.14 Å20 Å2
3---2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.15→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 1 290 5064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.18
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.318 --
Rwork0.263 --
obs-6134 85.1 %

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