[English] 日本語
Yorodumi
- PDB-4b5g: Substrate bound Neisseria AP endonuclease in absence of metal ion... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b5g
TitleSubstrate bound Neisseria AP endonuclease in absence of metal ions (crystal form 2)
Components
  • 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'
  • 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
  • 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: 2.75 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
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_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXODEOXYRIBONUCLEASE
B: EXODEOXYRIBONUCLEASE
C: EXODEOXYRIBONUCLEASE
U: 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
V: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'
W: 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
X: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'
Y: 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
Z: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)108,8979
Polymers108,8979
Non-polymers00
Water543
1
A: EXODEOXYRIBONUCLEASE
U: 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
V: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)36,2993
Polymers36,2993
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-4.8 kcal/mol
Surface area13330 Å2
MethodPISA
2
B: EXODEOXYRIBONUCLEASE
W: 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
X: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)36,2993
Polymers36,2993
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-7 kcal/mol
Surface area13270 Å2
MethodPISA
3
C: EXODEOXYRIBONUCLEASE
Y: 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3'
Z: 5'-D(*CP*GP*AP*TP*GP*GP*GP*TP*AP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)36,2993
Polymers36,2993
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-6.9 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.241, 75.241, 380.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.069609, 0.997532, -0.00924), (-0.996664, -0.069938, -0.042069), (-0.042611, 0.006281, 0.999072)-45.4093, -39.8299, 29.6007
2given(-0.983417, 0.179474, 0.026094), (0.179984, 0.983492, 0.018689), (-0.022309, 0.023076, -0.999485)-48.1955, -32.5194, -33.0469

-
Components

#1: Protein 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, exodeoxyribonuclease III
#2: DNA chain 5'-D(*GP*CP*TP*AP*CP*(3DR)P*CP*AP*TP*CP*GP)-3' / DNA 11MER CONTAINING ABASIC RESIDUE


Mass: 3185.076 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Source: (synth.) NEISSERIA MENINGITIDIS (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.28 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→75.2 Å / Num. obs: 29023 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.09

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: DEV_1084) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.75→44.076 Å / SU ML: 0.33 / σ(F): 1.38 / Phase error: 31.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1404 5.1 %
Rwork0.2319 --
obs0.2332 27545 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→44.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 1311 0 3 7584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037908
X-RAY DIFFRACTIONf_angle_d0.80810959
X-RAY DIFFRACTIONf_dihedral_angle_d19.1312988
X-RAY DIFFRACTIONf_chiral_restr0.0521122
X-RAY DIFFRACTIONf_plane_restr0.0021191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7501-2.84840.40391120.39271928X-RAY DIFFRACTION70
2.8484-2.96240.3781200.3382218X-RAY DIFFRACTION81
2.9624-3.09720.31161290.30632552X-RAY DIFFRACTION92
3.0972-3.26040.32321340.27722636X-RAY DIFFRACTION94
3.2604-3.46460.32691470.25682611X-RAY DIFFRACTION95
3.4646-3.7320.26811300.25322723X-RAY DIFFRACTION96
3.732-4.10730.29521590.23482744X-RAY DIFFRACTION98
4.1073-4.70110.20961660.19222806X-RAY DIFFRACTION99
4.7011-5.92060.23041390.19162891X-RAY DIFFRACTION100
5.9206-44.08120.22311680.22323032X-RAY DIFFRACTION98

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more