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- PDB-4b5m: Neisseria AP endonuclease bound to the substrate with a cytosine ... -

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Basic information

Entry
Database: PDB / ID: 4b5m
TitleNeisseria AP endonuclease bound to the substrate with a cytosine orphan base
Components
  • 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
  • 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'
  • 5'-D(*GP*CP*TP*AP*CP)-3'
  • PUTATIVE EXODEOXYRIBONUCLEASE
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / 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: 2.758 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 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE EXODEOXYRIBONUCLEASE
B: PUTATIVE EXODEOXYRIBONUCLEASE
C: PUTATIVE EXODEOXYRIBONUCLEASE
L: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
M: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
N: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
U: 5'-D(*GP*CP*TP*AP*CP)-3'
V: 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'
W: 5'-D(*GP*CP*TP*AP*CP)-3'
X: 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'
Y: 5'-D(*GP*CP*TP*AP*CP)-3'
Z: 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)108,64212
Polymers108,64212
Non-polymers00
Water00
1
A: PUTATIVE EXODEOXYRIBONUCLEASE
L: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
U: 5'-D(*GP*CP*TP*AP*CP)-3'
V: 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)36,2144
Polymers36,2144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-16.9 kcal/mol
Surface area13140 Å2
MethodPISA
2
B: PUTATIVE EXODEOXYRIBONUCLEASE
M: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
W: 5'-D(*GP*CP*TP*AP*CP)-3'
X: 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)36,2144
Polymers36,2144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-14 kcal/mol
Surface area13230 Å2
MethodPISA
3
C: PUTATIVE EXODEOXYRIBONUCLEASE
N: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
Y: 5'-D(*GP*CP*TP*AP*CP)-3'
Z: 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)36,2144
Polymers36,2144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-13.8 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.050, 77.050, 382.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:257 )
211CHAIN B AND (RESSEQ 1:257 )
311CHAIN C AND (RESSEQ 1:257 )

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Components

#1: Protein PUTATIVE EXODEOXYRIBONUCLEASE / NEISSERIA AP ENDONUCLEASE


Mass: 29699.594 Da / Num. of mol.: 3
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
#2: DNA chain 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'


Mass: 1660.107 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)
#3: DNA chain 5'-D(*GP*CP*TP*AP*CP)-3'


Mass: 1480.012 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)
#4: DNA chain 5'-D(*CP*GP*AP*TP*GP*CP*GP*TP*AP*GP*CP)-3'


Mass: 3374.210 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.93 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→50.1 Å / Num. obs: 30548 / % possible obs: 98.5 % / Observed criterion σ(I): 2.5 / Redundancy: 6.4 % / Biso Wilson estimate: 68.73 Å2 / Rmerge(I) obs: 0.06

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Processing

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

Resolution: 2.758→50.102 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 31.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 1529 5.1 %
Rwork0.2302 --
obs0.2325 30270 97.56 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.463 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.0887 Å20 Å20 Å2
2--14.0887 Å20 Å2
3----28.1773 Å2
Refinement stepCycle: LAST / Resolution: 2.758→50.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6257 1305 0 0 7562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098119
X-RAY DIFFRACTIONf_angle_d1.00510917
X-RAY DIFFRACTIONf_dihedral_angle_d21.3832974
X-RAY DIFFRACTIONf_chiral_restr0.0661120
X-RAY DIFFRACTIONf_plane_restr0.0031188
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2077X-RAY DIFFRACTIONPOSITIONAL
12B2077X-RAY DIFFRACTIONPOSITIONAL0.023
13C2077X-RAY DIFFRACTIONPOSITIONAL0.024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.758-2.85660.49651680.39392838X-RAY DIFFRACTION99
2.8566-2.97090.37551460.34242850X-RAY DIFFRACTION99
2.9709-3.10610.39371510.32835X-RAY DIFFRACTION99
3.1061-3.26990.29991320.27562847X-RAY DIFFRACTION99
3.2699-3.47470.33481590.27692851X-RAY DIFFRACTION98
3.4747-3.74290.31431250.29872635X-RAY DIFFRACTION90
3.7429-4.11940.27561620.23792804X-RAY DIFFRACTION96
4.1194-4.71510.22291700.16762918X-RAY DIFFRACTION99
4.7151-5.9390.22211490.18193035X-RAY DIFFRACTION100
5.939-50.110.24571670.19373128X-RAY DIFFRACTION97

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