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- PDB-2voa: Structure of an AP Endonuclease from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 2voa
TitleStructure of an AP Endonuclease from Archaeoglobus fulgidus
Components
  • 5'-D(*CP*GP*GP*CP*TP*AP*CP*CP*GP*CP)-3'
  • 5'-D(*GP*CP*GP*GP*TP*AP*GP*CP*CP*GP)-3'
  • EXODEOXYRIBONUCLEASE III
KeywordsLYASE / EXOIII / AP ENDONUCLEASE / ARCHAEOGLOBUS FULGIDUS
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / endonuclease activity / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Exodeoxyribonuclease III-like / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily ...Exodeoxyribonuclease III-like / AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Exodeoxyribonuclease III (XthA)
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKuettner, E.B. / Schmiedel, R. / Greiner-Stoffele, T. / Strater, N.
Citation
Journal: DNA Repair / Year: 2009
Title: Structure and Function of the Abasic Site Specificity Pocket of an Ap Endonuclease from Archaeoglobus Fulgidus.
Authors: Schmiedel, R. / Kuettner, E.B. / Keim, A. / Strater, N. / Greiner-Stoffele, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and Preliminary X-Ray Characterization of Two Thermostable DNA Nucleases
Authors: Kuettner, E.B. / Pfeifer, S. / Keim, A. / Greiner-Stoffele, T. / Strater, N.
History
DepositionFeb 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_entity_src_syn / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Sep 1, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range
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_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.sheet_id
Revision 1.6Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXODEOXYRIBONUCLEASE III
B: EXODEOXYRIBONUCLEASE III
C: 5'-D(*GP*CP*GP*GP*TP*AP*GP*CP*CP*GP)-3'
D: 5'-D(*CP*GP*GP*CP*TP*AP*CP*CP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)65,7124
Polymers65,7124
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-7 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.786, 60.817, 72.349
Angle α, β, γ (deg.)90.00, 91.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EXODEOXYRIBONUCLEASE III / AF_EXO / XTHA


Mass: 29810.215 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Description: DSM4304 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI B(DE3)-RIL
References: UniProt: O29675, DNA-(apurinic or apyrimidinic site) lyase
#2: DNA chain 5'-D(*GP*CP*GP*GP*TP*AP*GP*CP*CP*GP)-3'


Mass: 3086.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*CP*GP*GP*CP*TP*AP*CP*CP*GP*CP)-3'


Mass: 3005.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 217 TO GLY ENGINEERED RESIDUE IN CHAIN B, VAL 217 TO GLY
Sequence detailsV217G

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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: 2.2 Å3/Da / Density % sol: 43.67 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: HANGING-DROP METHOD AT 292 K WITH 1 MICROLITER OF RESERVOIR AND PROTEIN SOLUTION EACH. TRIS-HCL PH 8.5. PROTEIN: 17 MG/ML AF_EXO, 0.53 MM DS-DNA, 9 MM MES-NAOH PH 6, 0.28 M NACL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 10, 2005 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 64871 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.5
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKO

1ako


Resolution: 1.7→29.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.57 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED 5'-END PHOSPHATES OF DNA WERE NOT MODELED. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1314 2 %RANDOM
Rwork0.198 ---
obs0.198 63550 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20.17 Å2
2---1.32 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 404 0 220 4828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224787
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3982.076570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9585516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46923.146213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1215762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1441537
X-RAY DIFFRACTIONr_chiral_restr0.0950.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023533
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22033
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23230
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6751.52651
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04324207
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74132556
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6734.52363
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.466 100
Rwork0.378 4639
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.35390.4192-0.32351.4669-0.12181.60460.0999-0.09290.0460.0666-0.0282-0.0033-0.01610.049-0.0717-0.1416-0.0147-0.007-0.1525-0.0069-0.12532.3288-0.396214.5146
21.9263-0.08520.64263.40860.7542.3797-0.0439-0.19420.14830.25980.0572-0.04290.08890.0297-0.0133-0.1130.02870.0211-0.0716-0.0004-0.0529-0.055-2.6433-20.2867
32.41360.72442.69032.73333.77896.50810.2441-0.5903-0.35670.5286-0.16360.12920.618-0.5516-0.08050.0973-0.0766-0.03520.10520.04010.054140.6327-3.295740.9635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 257
2X-RAY DIFFRACTION2B1 - 257
3X-RAY DIFFRACTION3C1 - 10
4X-RAY DIFFRACTION3D1 - 10

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