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- PDB-4b5f: Substrate bound Neisseria AP endonuclease in absence of metal ion... -

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Basic information

Entry
Database: PDB / ID: 4b5f
TitleSubstrate bound Neisseria AP endonuclease in absence of metal ions (crystal form 1)
Components
  • 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*CP)-3'
  • 5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3'
  • PUTATIVE EXODEOXYRIBONUCLEASE
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA binding / metal ion binding
Similarity search - Function
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 / DNA (> 10) / : / Exodeoxyribonuclease
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.005 Å
AuthorsLu, D. / Silhan, J. / MacDonald, J.T. / Carpenter, E.P. / Jensen, K. / Tang, C.M. / Baldwin, G.S. / Freemont, P.S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2012
Title: Structural basis for the recognition and cleavage of abasic DNA in Neisseria meningitidis.
Authors: Lu, D. / Silhan, J. / MacDonald, J.T. / Carpenter, E.P. / Jensen, K. / Tang, C.M. / Baldwin, G.S. / Freemont, P.S.
History
DepositionAug 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3May 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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE EXODEOXYRIBONUCLEASE
U: 5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3'
V: 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)36,2993
Polymers36,2993
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-11 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.789, 67.789, 125.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2257-

HOH

21U-2023-

HOH

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Components

#1: Protein PUTATIVE EXODEOXYRIBONUCLEASE / NEISSERIA AP ENDONUCLEASE


Mass: 29699.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: C9X331, UniProt: Q7DD47*PLUS, exodeoxyribonuclease III
#2: DNA chain 5'-D(*GP*CP*TP*AP*CP*3DRP*GP*AP*TP*CP*GP)-3' / DNA 11MER CONTAINING ABASIC RESIDUE


Mass: 3225.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)
#3: DNA chain 5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*CP)-3'


Mass: 3374.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→33.8 Å / Num. obs: 20280 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.11

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.005→33.895 Å / SU ML: 0.24 / σ(F): 1.35 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2268 2065 10.28 %
Rwork0.1776 --
obs0.1825 20280 99.96 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.6062 Å20 Å20 Å2
2---1.6062 Å20 Å2
3---3.2124 Å2
Refinement stepCycle: LAST / Resolution: 2.005→33.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 437 0 326 2835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042763
X-RAY DIFFRACTIONf_angle_d0.63755
X-RAY DIFFRACTIONf_dihedral_angle_d17.0951030
X-RAY DIFFRACTIONf_chiral_restr0.038384
X-RAY DIFFRACTIONf_plane_restr0.001398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0047-2.07630.27362010.21221768X-RAY DIFFRACTION100
2.0763-2.15940.27311980.19741782X-RAY DIFFRACTION100
2.1594-2.25770.24892190.1831779X-RAY DIFFRACTION100
2.2577-2.37670.23012040.17531768X-RAY DIFFRACTION100
2.3767-2.52560.23741900.18311823X-RAY DIFFRACTION100
2.5256-2.72050.24382110.18961799X-RAY DIFFRACTION100
2.7205-2.99410.26052320.19151777X-RAY DIFFRACTION100
2.9941-3.4270.23861790.17241875X-RAY DIFFRACTION100
3.427-4.31630.18162100.15831862X-RAY DIFFRACTION100
4.3163-33.89930.19142210.16031982X-RAY DIFFRACTION100

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