[English] 日本語
Yorodumi
- PDB-4hno: High resolution crystal structure of DNA Apurinic/apyrimidinic (A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hno
TitleHigh resolution crystal structure of DNA Apurinic/apyrimidinic (AP) endonuclease IV Nfo from Thermatoga maritima
ComponentsProbable endonuclease 4
KeywordsHYDROLASE / endonuclease 4 / endodeoxyribonuclease IV / endo IV / nfo / metalloprotein / DNA damage / DNA repair / base excision repair
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / DNA binding / zinc ion binding
Similarity search - Function
AP endonucleases family 2 signature 1. / AP endonucleases family 2 signature 2. / AP endonuclease 2, zinc binding site / AP endonucleases family 2 signature 3. / AP endonucleases family 2 profile. / AP endonuclease 2 / AP endonuclease family 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel ...AP endonucleases family 2 signature 1. / AP endonucleases family 2 signature 2. / AP endonuclease 2, zinc binding site / AP endonucleases family 2 signature 3. / AP endonucleases family 2 profile. / AP endonuclease 2 / AP endonuclease family 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Probable endonuclease 4
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.9194 Å
AuthorsShin, D.S. / Hosfield, D.J. / Arvai, A.S. / Tsutakawa, S.E. / Tainer, J.A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes.
Authors: Tsutakawa, S.E. / Shin, D.S. / Mol, C.D. / Izumi, T. / Arvai, A.S. / Mantha, A.K. / Szczesny, B. / Ivanov, I.N. / Hosfield, D.J. / Maiti, B. / Pique, M.E. / Frankel, K.A. / Hitomi, K. / ...Authors: Tsutakawa, S.E. / Shin, D.S. / Mol, C.D. / Izumi, T. / Arvai, A.S. / Mantha, A.K. / Szczesny, B. / Ivanov, I.N. / Hosfield, D.J. / Maiti, B. / Pique, M.E. / Frankel, K.A. / Hitomi, K. / Cunningham, R.P. / Mitra, S. / Tainer, J.A.
History
DepositionOct 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,22411
Polymers32,5511
Non-polymers67310
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.370, 123.370, 35.395
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Probable endonuclease 4 / Endodeoxyribonuclease IV / Endonuclease IV


Mass: 32550.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: nfo, TM_0362 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYJ7, deoxyribonuclease IV

-
Non-polymers , 7 types, 437 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Tris-HCl pH 9.0, 4 mM DTT, 1.5% saturated MgSO4, 16% ethylene glycol, 20% mPEG2K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.78 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 1999
RadiationMonochromator: MIRRORS POLAR 0.000 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 26.51 / Number: 582465 / Rmerge(I) obs: 0.053 / Χ2: 1.21 / D res high: 0.92 Å / D res low: 30 Å / Num. obs: 204938 / % possible obs: 95.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
2.113096.610.0441.203
1.672.1197.710.0561.201
1.461.6799.410.0981.251
1.331.4698.810.1361.24
1.231.3395.310.061.649
1.161.2395.810.0741.547
1.11.1696.410.0891.387
1.051.196.610.1181.215
1.011.0596.710.1671.051
0.981.0195.410.2420.95
0.950.9893.810.3240.874
0.920.9588.610.420.799
ReflectionResolution: 0.9194→30 Å / Num. all: 213629 / Num. obs: 204938 / % possible obs: 95.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 2.84 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.053 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
0.9194-0.950.42188.6
0.95-0.980.324193.8
0.98-1.010.242195.4
1.01-1.050.167196.7
1.05-1.10.118196.6
1.1-1.160.089196.4
1.16-1.230.074195.8
1.23-1.330.06195.3
1.33-1.460.136198.8
1.46-1.670.098199.4
1.67-2.110.056197.7
2.11-300.044196.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.52 / Cor.coef. Fo:Fc: 0.241
Highest resolutionLowest resolution
Translation4.5 Å8 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
EPMR2.1phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QTW

1qtw


Resolution: 0.9194→24.511 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.06 / σ(F): 1.34 / Phase error: 11.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.139 10253 5 %
Rwork0.1248 --
obs0.1255 204917 95.92 %
all-204931 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.0195 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 0.9194→24.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 27 427 2721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172475
X-RAY DIFFRACTIONf_angle_d1.3113352
X-RAY DIFFRACTIONf_dihedral_angle_d12.775961
X-RAY DIFFRACTIONf_chiral_restr0.08349
X-RAY DIFFRACTIONf_plane_restr0.008431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9194-0.92980.23962880.21965717X-RAY DIFFRACTION84
0.9298-0.94080.21953150.19726078X-RAY DIFFRACTION91
0.9408-0.95230.18813130.1786184X-RAY DIFFRACTION92
0.9523-0.96430.17833370.17146337X-RAY DIFFRACTION94
0.9643-0.9770.17743210.1616341X-RAY DIFFRACTION94
0.977-0.99040.16533420.15546415X-RAY DIFFRACTION96
0.9904-1.00450.15733190.14746459X-RAY DIFFRACTION95
1.0045-1.01950.14943330.13586473X-RAY DIFFRACTION96
1.0195-1.03550.14983310.12556517X-RAY DIFFRACTION96
1.0355-1.05240.12933330.11846537X-RAY DIFFRACTION97
1.0524-1.07060.13453720.11136456X-RAY DIFFRACTION96
1.0706-1.090.12193470.1046473X-RAY DIFFRACTION97
1.09-1.1110.10953490.10336539X-RAY DIFFRACTION96
1.111-1.13370.11413620.09816480X-RAY DIFFRACTION97
1.1337-1.15830.11483340.09466497X-RAY DIFFRACTION96
1.1583-1.18530.11073720.09746459X-RAY DIFFRACTION96
1.1853-1.21490.11883590.16470X-RAY DIFFRACTION96
1.2149-1.24780.10713180.09766447X-RAY DIFFRACTION95
1.2478-1.28450.11513290.16451X-RAY DIFFRACTION95
1.2845-1.32590.1143270.09996434X-RAY DIFFRACTION95
1.3259-1.37330.11863330.16606X-RAY DIFFRACTION98
1.3733-1.42830.11593840.10016719X-RAY DIFFRACTION100
1.4283-1.49330.12133550.09816750X-RAY DIFFRACTION100
1.4933-1.5720.1113470.10136741X-RAY DIFFRACTION100
1.572-1.67050.14783140.11876793X-RAY DIFFRACTION99
1.6705-1.79940.13523660.12436643X-RAY DIFFRACTION98
1.7994-1.98050.14613370.1226661X-RAY DIFFRACTION97
1.9805-2.26690.13293630.12116592X-RAY DIFFRACTION97
2.2669-2.85530.14363880.12756778X-RAY DIFFRACTION99
2.8553-24.51980.15993650.15516617X-RAY DIFFRACTION94

+
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