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- PDB-3ga2: Crystal structure of the Endonuclease_V (BSU36170) from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 3ga2
TitleCrystal structure of the Endonuclease_V (BSU36170) from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR624
ComponentsEndonuclease V
KeywordsHYDROLASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Cytoplasm / DNA damage / DNA repair / Endonuclease / Magnesium / Nuclease
Function / homology
Function and homology information


deoxyribonuclease V / deoxyribonuclease V activity / RNA endonuclease activity, producing 5'-phosphomonoesters / single-stranded RNA binding / DNA repair / magnesium ion binding / cytoplasm
Similarity search - Function
Endonuclease V / Endonuclease V / archaeoglobus fulgidus dsm 4304 fold / archaeoglobus fulgidus dsm 4304 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsForouhar, F. / Abashidze, M. / Hussain, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owens, L. ...Forouhar, F. / Abashidze, M. / Hussain, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owens, L. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Endonuclease_V (BSU36170) from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR624
Authors: Forouhar, F. / Abashidze, M. / Hussain, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owens, L. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / ...Authors: Forouhar, F. / Abashidze, M. / Hussain, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Cunningham, K. / Ma, L.-C. / Owens, L. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionFeb 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author / entity_src_gen
Item: _audit_author.name / _citation_author.name / _entity_src_gen.pdbx_gene_src_gene
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease V


Theoretical massNumber of molelcules
Total (without water)28,3601
Polymers28,3601
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.806, 83.861, 52.287
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Endonuclease V / / Deoxyinosine 3'endonuclease / Deoxyribonuclease V / DNase V


Mass: 28359.732 Da / Num. of mol.: 1 / Mutation: G42T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: str. 168 / Gene: nfi, ywqL / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P96724, deoxyribonuclease V
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 16% PEG 3350 and 200 mM ammonium tartrate., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97902 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 30730 / Num. obs: 30177 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.065 / Net I/σ(I): 20.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3061 / Rsym value: 0.303 / % possible all: 88.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBthen SOLVE/RESOLVEphasing
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→19.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 98764.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2555 9.7 %RANDOM
Rwork0.2 ---
all0.202 30635 --
obs0.2 26224 85.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 94.6304 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å20 Å20 Å2
2---5.32 Å20 Å2
3---7.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 0 152 2049
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.17 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.226 188 10.1 %
Rwork0.195 1676 -
obs-1676 61.1 %

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