[English] 日本語
Yorodumi
- PDB-3ta7: Zinc bound structure of an archaeal member of the LigD 3'-phospho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ta7
TitleZinc bound structure of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family
ComponentsATP-dependent DNA ligase, N-terminal domain protein
KeywordsHYDROLASE / 3'-phosphoesterase
Function / homologyDNA ligase D, 3'-phosphoesterase domain / DNA polymerase Ligase (LigD) / ligase activity / metal ion binding / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / ATP-dependent DNA ligase, N-terminal domain protein
Function and homology information
Biological speciesCandidatus Korarchaeum cryptofilum OPF8 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsDas, U. / Smith, P. / Shuman, S.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural insights to the metal specificity of an archaeal member of the LigD 3'-phosphoesterase DNA repair enzyme family.
Authors: Das, U. / Smith, P. / Shuman, S.
History
DepositionAug 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: ATP-dependent DNA ligase, N-terminal domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1174
Polymers13,8501
Non-polymers2673
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.740, 58.570, 32.980
Angle α, β, γ (deg.)90.00, 102.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ATP-dependent DNA ligase, N-terminal domain protein


Mass: 13850.097 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Korarchaeum cryptofilum OPF8 (archaea)
Gene: Kcr_0736 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1L4V6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Crystallization was carried out in hanging-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 0.7 mM Cko and 10 mM ZnCl2 and reservoir solution containing 20% PEG ...Details: Crystallization was carried out in hanging-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 0.7 mM Cko and 10 mM ZnCl2 and reservoir solution containing 20% PEG 3350 and 0.2 M Na2HPO4 , pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.282 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2011
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.48→32.21 Å / Num. all: 17231 / Num. obs: 16869 / % possible obs: 97.9 % / Observed criterion σ(F): -99 / Observed criterion σ(I): -99 / Redundancy: 2.8 % / Rsym value: 0.028 / Net I/σ(I): 16.8
Reflection shellHighest resolution: 1.48 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 16.8 / Rsym value: 0.028 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_833)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→29.285 Å / SU ML: 0.28 / σ(F): 1.38 / Phase error: 17.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 1737 10.31 %RANDOM
Rwork0.1471 ---
obs0.1503 16852 97.78 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.982 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7302 Å2-0 Å22.4112 Å2
2---2.0522 Å2-0 Å2
3---1.322 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 13 207 1187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131101
X-RAY DIFFRACTIONf_angle_d1.4911491
X-RAY DIFFRACTIONf_dihedral_angle_d13.855446
X-RAY DIFFRACTIONf_chiral_restr0.095151
X-RAY DIFFRACTIONf_plane_restr0.007191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.52360.21791310.16661066X-RAY DIFFRACTION84
1.5236-1.57280.22861450.15811241X-RAY DIFFRACTION97
1.5728-1.6290.18461560.15191261X-RAY DIFFRACTION99
1.629-1.69420.1911630.15561248X-RAY DIFFRACTION99
1.6942-1.77130.19371390.16161268X-RAY DIFFRACTION99
1.7713-1.86460.19911360.16331282X-RAY DIFFRACTION99
1.8646-1.98140.18381530.1481289X-RAY DIFFRACTION99
1.9814-2.13440.18591400.151291X-RAY DIFFRACTION100
2.1344-2.34910.20971430.14821286X-RAY DIFFRACTION100
2.3491-2.68880.19531430.15381282X-RAY DIFFRACTION100
2.6888-3.38680.15951440.13521289X-RAY DIFFRACTION99
3.3868-29.29070.14031440.13661312X-RAY DIFFRACTION99

+
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://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