[English] 日本語
Yorodumi
- PDB-1hd7: A Second Divalent Metal Ion in the Active Site of a New Crystal F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hd7
TitleA Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism
ComponentsDNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
KeywordsDNA REPAIR / ENDONUCLEASE / APE1 / HAP1 / REF-1
Function / homology
Function and homology information


Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity ...Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / double-stranded DNA exodeoxyribonuclease activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / uracil DNA N-glycosylase activity / DNA catabolic process / 3'-5'-DNA exonuclease activity / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / regulation of apoptotic process / DNA recombination / endonuclease activity / chromosome, telomeric region / damaged DNA binding / transcription coactivator activity / oxidoreductase activity / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / 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 ...AP endonucleases family 1 signature 2. / AP endonuclease 1, conserved site / AP endonucleases family 1 signature 3. / 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
LEAD (II) ION / DNA repair nuclease/redox regulator APEX1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBeernink, P.T. / Segelke, B.W. / Rupp, B.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism
Authors: Beernink, P.T. / Segelke, B.W. / Hadi, M.Z. / Erzberger, J.P. / Wilson III, D.M. / Rupp, B.
History
DepositionNov 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8142
Polymers35,6061
Non-polymers2071
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)128.390, 44.850, 78.140
Angle α, β, γ (deg.)90.00, 124.54, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE / AP ENDONUCLEASE 1 / HAP1 / REF1 / APE1


Mass: 35606.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: ALL / Cell: ALL / Organelle: NUCLEUS / Plasmid: PET11D / Gene (production host): APE1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase
#2: Chemical ChemComp-PB / LEAD (II) ION


Mass: 207.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENDONUCLEOLYTIC CLEAVAGE NEAR APURINIC OR APYRIMIDINIC SITES TO PRODUCTS WITH 5'-PHOSPHATE. REPAIRS ...ENDONUCLEOLYTIC CLEAVAGE NEAR APURINIC OR APYRIMIDINIC SITES TO PRODUCTS WITH 5'-PHOSPHATE. REPAIRS OXIDATIVE DNA DAMAGES IN VITRO. REMOVES THE BLOCKING GROUPS FROM THE 3' TERMINI OF THE DNA STRAND BREAKS GENERATED BY IONIZING RADIATIONS AND BLEOMYCIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 4.5
Details: 0.1M NAOAC PH 4.6, 25% PEG 4K, 1 MM PB(II)OAC, 10-12 MG/ML PROTEIN.
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-12 mg/mlprotein1drop
20.1 Msodium acetate1reservoir
325 %(w/v)PEG40001reservoir
41 mMlead (II) acetate1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.2398
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 1999 / Details: DUAL CRYSTAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 34905 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.68 Å2 / Rsym value: 0.082 / Net I/σ(I): 6.6
Reflection shellResolution: 1.95→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.5 / % possible all: 99.2
Reflection
*PLUS
Num. measured all: 91465 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.471

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TO BE PUBLISHED

Resolution: 1.95→25 Å / SU B: 3.7 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2699 10 %RANDOM
Rwork0.205 ---
obs-26771 92.2 %-
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 1 288 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0690.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.82
X-RAY DIFFRACTIONp_mcangle_it2.73
X-RAY DIFFRACTIONp_scbond_it2.22
X-RAY DIFFRACTIONp_scangle_it3.43
X-RAY DIFFRACTIONp_plane_restr0.03
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2610.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1250.3
X-RAY DIFFRACTIONp_planar_tor8.47
X-RAY DIFFRACTIONp_staggered_tor18.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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