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- PDB-4b5i: Product complex of Neisseria AP endonuclease in presence of metal ions -

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Basic information

Entry
Database: PDB / ID: 4b5i
TitleProduct complex of Neisseria AP endonuclease in presence of metal ions
Components
  • 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
  • 5'-D(*CP*GP*AP*TP*GP*GP*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: 2.555 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 1.1Oct 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 / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_conn_type.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: PUTATIVE EXODEOXYRIBONUCLEASE
U: 5'-D(*GP*CP*TP*AP*CP)-3'
V: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'
X: 5'-D(*3DRP*CP*AP*TP*CP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3095
Polymers36,2544
Non-polymers551
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-18.5 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.090, 69.090, 119.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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

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DNA chain , 3 types, 3 molecules UVX

#2: DNA chain 5'-D(*GP*CP*TP*AP*CP)-3'


Mass: 1480.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)
#3: DNA chain 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'


Mass: 3414.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)
#4: DNA chain 5'-D(*3DRP*CP*AP*TP*CP*GP)-3' / DNA 6MER CONTAINING ABASIC RESIDUE


Mass: 1660.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)

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Non-polymers , 2 types, 33 molecules

#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 37.55 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9797
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.55→59.8 Å / Num. obs: 9098 / % possible obs: 99.2 % / Observed criterion σ(I): 1.2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.07

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Processing

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

Resolution: 2.555→45.231 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2515 448 4.9 %
Rwork0.2047 --
obs0.207 9098 91.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.214 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4179 Å20 Å20 Å2
2--2.4179 Å20 Å2
3----4.8359 Å2
Refinement stepCycle: LAST / Resolution: 2.555→45.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 438 1 32 2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032683
X-RAY DIFFRACTIONf_angle_d0.5363627
X-RAY DIFFRACTIONf_dihedral_angle_d16.366987
X-RAY DIFFRACTIONf_chiral_restr0.035371
X-RAY DIFFRACTIONf_plane_restr0.001393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5548-2.92440.37011310.29972538X-RAY DIFFRACTION83
2.9244-3.68420.28721560.21612894X-RAY DIFFRACTION93
3.6842-45.23770.211610.1793218X-RAY DIFFRACTION98
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)
11.517-1.4469-0.38932.92161.1931.3782-0.4045-0.45480.27830.79620.5422-0.19190.0752-0.14130.05240.28220.1041-0.060.3077-0.07330.1131-13.488929.191514.2242
20.295-0.3889-0.18740.50760.16430.1889-0.2017-0.467-0.47420.2581-0.07880.1421-0.4416-0.37480.00010.34650.13510.01460.36050.01090.4093-21.856337.05278.0559
32.0593-0.04140.55021.27181.02611.7643-0.3194-0.3924-0.06830.0176-0.22820.1855-0.0421-0.4349-0.67480.04550.00140.14860.30410.03460.1328-25.682923.55098.1398
40.2223-0.0904-0.26310.42921.13053.0281-0.1320.09780.11450.23730.0360.32430.827-0.2615-0.01680.1791-0.08490.02650.2835-0.05660.4941-31.045817.88722.0998
51.04691.3158-0.64181.8183-0.07863.6570.706-0.2861-0.7002-0.149-0.29340.45280.0356-0.02270.18460.12450.0162-0.20710.4311-0.09470.356-28.913933.3065-5.7231
61.18460.0453-0.33291.911-0.23591.604-0.11670.1713-0.5277-0.74710.08380.51240.6665-0.35350.00060.3420.0043-0.02690.2141-0.03490.2898-18.994115.1237-4.6916
70.5965-0.6561-0.76864.7541.01861.929-0.216-0.027-0.2011-0.18610.5648-0.5320.30970.08270.19670.12450.0701-0.04350.2731-0.08880.2406-9.12420.54850.1825
80.0496-0.04590.00310.0413-0.0007-0.00060.15161.47770.22020.50650.578-0.14150.6407-0.28180.0021.2308-0.11270.37040.65060.08960.8651-18.88869.235922.9656
90.0616-0.0646-0.00640.0629-0.00190.01520.4130.5403-0.6861-0.11550.05290.19060.3295-0.22360.00160.89180.10770.0871.23290.63121.0189-14.1052-7.74956.8885
100.2630.1964-0.07740.1366-0.05780.01980.3052-0.6113-1.25320.9066-0.68850.3011-0.2996-0.03130.00120.86540.33770.00320.7224-0.23580.6601-11.53111.26220.6194
110.50310.29030.12470.2145-0.0630.3190.3411-0.2499-0.49390.098-0.2982-0.61080.21720.3943-0.00060.90540.261-0.06760.5113-0.00270.7564-9.7163-1.03496.2878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:70)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 71:85)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 86:119)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 120:136)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 137:142)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 143:196)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 197:256)
8X-RAY DIFFRACTION8(CHAIN U AND RESID 31:35)
9X-RAY DIFFRACTION9(CHAIN V AND RESID 42:46)
10X-RAY DIFFRACTION10(CHAIN V AND RESID 47:52)
11X-RAY DIFFRACTION11(CHAIN X AND RESID 36:41)

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