[English] 日本語
Yorodumi
- PDB-3p4h: Structures of archaeal members of the LigD 3'-phosphoesterase DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p4h
TitleStructures of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily
ComponentsATP-dependent DNA ligase, N-terminal domain protein
KeywordsHYDROLASE / Phosphoesterase / Metalloenzyme / Manganese / beta barrel / phosphatase
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 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsSmith, P. / Nair, P.A. / Das, U. / Zhu, H. / Shuman, S.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structures and activities of archaeal members of the LigD 3'-phosphoesterase DNA repair enzyme superfamily.
Authors: Smith, P. / Nair, P.A. / Das, U. / Zhu, H. / Shuman, S.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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_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)14,1064
Polymers13,8501
Non-polymers2563
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.769, 58.458, 33.180
Angle α, β, γ (deg.)90.00, 102.25, 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 (archaea)
Strain: OPF8 / Gene: Kcr_0736 / Plasmid: pET28bSmt3His10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: B1L4V6
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#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.: 216 / 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: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 0.7 mM Cko and 1.8 mM MnCl2 and reservoir solution containing 20% PEG ...Details: Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 0.7 mM Cko and 1.8 mM MnCl2 and reservoir solution containing 20% PEG 3350 and 0.2 M Na2HPO4 , pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 2, 2010
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. all: 42013 / Num. obs: 40543 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 42
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.07 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N9B

3n9b


Resolution: 1.1→23.397 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1647 4161 10.27 %Random
Rwork0.1321 ---
obs0.1354 40516 96.49 %-
all-42013 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.996 Å2 / ksol: 0.293 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2895 Å2-0 Å21.2613 Å2
2---1.9815 Å2-0 Å2
3---0.4927 Å2
Refinement stepCycle: LAST / Resolution: 1.1→23.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 13 216 1192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111213
X-RAY DIFFRACTIONf_angle_d1.4061659
X-RAY DIFFRACTIONf_dihedral_angle_d13.155501
X-RAY DIFFRACTIONf_chiral_restr0.095166
X-RAY DIFFRACTIONf_plane_restr0.007218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.1-1.13930.20644010.18833439343992
1.1393-1.18490.1983850.15723479347992
1.1849-1.23890.2143900.15993512351293
1.2389-1.30420.19784010.15163567356795
1.3042-1.38590.18394290.12953637363797
1.3859-1.49290.17024360.12233659365998
1.4929-1.6430.15254390.11123719371999
1.643-1.88070.16214330.1183737373799
1.8807-2.36910.16014230.123837723772100
2.3691-23.40260.15224240.134338343834100

+
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