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- PDB-4b20: Structural basis of DNA loop recognition by Endonuclease V -

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Basic information

Entry
Database: PDB / ID: 4b20
TitleStructural basis of DNA loop recognition by Endonuclease V
Components
  • 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
  • 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
  • ENDONUCLEASE V
KeywordsHYDROLASE
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
DNA / Endonuclease V
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.75 Å
AuthorsRosnes, I. / Rowe, A.D. / Forstrom, R.J. / Alseth, I. / Bjoras, M. / Dalhus, B.
CitationJournal: Structure / Year: 2013
Title: Structural Basis of DNA Loop Recognition by Endonuclease V.
Authors: Rosnes, I. / Rowe, A.D. / Vik, E.S. / Forstrom, R.J. / Alseth, I. / Bjoras, M. / Dalhus, B.
History
DepositionJul 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDONUCLEASE V
B: ENDONUCLEASE V
C: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
D: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
F: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
G: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6378
Polymers61,5896
Non-polymers492
Water1,42379
1
A: ENDONUCLEASE V
C: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
D: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8194
Polymers30,7943
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDONUCLEASE V
F: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
G: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8194
Polymers30,7943
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: ENDONUCLEASE V
C: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
D: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
hetero molecules

A: ENDONUCLEASE V
C: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
D: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6378
Polymers61,5896
Non-polymers492
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area7010 Å2
ΔGint-37.4 kcal/mol
Surface area21580 Å2
MethodPISA
4
B: ENDONUCLEASE V
F: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
G: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
hetero molecules

B: ENDONUCLEASE V
F: 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'
G: 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6378
Polymers61,5896
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area6780 Å2
ΔGint-33.6 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.231, 135.370, 194.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ENDONUCLEASE V / DEOXYINOSINE 3'ENDONUCLEASE / DEOXYRIBONUCLEASE V / DNASE V


Mass: 25635.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X2H9, deoxyribonuclease V
#2: DNA chain 5'-D(*GP*CP*GP*AP*CP*AP*GP)-3'


Mass: 2147.437 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*TP*CP*TP*TP*GP*TP*CP*GP*CP)-3'


Mass: 3010.978 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.04 Å3/Da / Density % sol: 59.22 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.75→60 Å / Num. obs: 19328 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.13 / Net I/σ(I): 10.6
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.45 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.75→60 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2906 843 4.3 %RANDOM
Rwork0.2274 ---
obs0.2274 17361 88.9 %-
Solvent computationBsol: 41.4369 Å2 / ksol: 0.330552 e/Å3
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1--33.456 Å20 Å20 Å2
2--28.833 Å20 Å2
3---4.623 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati sigma a0.59 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.75→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 629 2 79 4290
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0073
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_deg1.349
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.45
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.204
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.82.5
LS refinement shellResolution: 2.75→2.85 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 63 4.7 %
Rwork0.41 1283 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAMINOSIN.TOP
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:INOSIN.PARAMCNS_TOPPAR:ION.TOP

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