[English] 日本語
Yorodumi
- PDB-5dmp: Structure of the Archaeal NHEJ Phosphoesterase from Methanocella ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dmp
TitleStructure of the Archaeal NHEJ Phosphoesterase from Methanocella paludicola.
ComponentsUncharacterized protein
KeywordsHYDROLASE / Archaeal Proteins / Biocatalysis / DNA Repair Enzymes / Phosphoric Diester Hydrolases / Phosphoric Monoester Hydrolases
Function / homologyDNA ligase D, 3'-phosphoesterase domain / DNA Ligase D 3'-phosphoesterase domain / oxido(dioxo)vanadium / DNA ligase D 3'-phosphoesterase domain-containing protein
Function and homology information
Biological speciesMethanocella paludicola (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.793 Å
AuthorsBrissett, N.C. / Bartlett, E.J. / Doherty, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council(BB/J018643/1) United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Molecular basis for DNA strand displacement by NHEJ repair polymerases.
Authors: Bartlett, E.J. / Brissett, N.C. / Plocinski, P. / Carlberg, T. / Doherty, A.J.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,62110
Polymers19,0631
Non-polymers5589
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint6 kcal/mol
Surface area9240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.070, 57.070, 105.041
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Uncharacterized protein


Mass: 19062.793 Da / Num. of mol.: 1 / Fragment: UNP residues 30-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocella paludicola (archaea) / Gene: MCP_2127 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D1Z0H7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM magnesium sulfate, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.793→49.424 Å / Num. all: 18976 / Num. obs: 18976 / % possible obs: 98.9 % / Redundancy: 5 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.056 / Rsym value: 0.05 / Net I/av σ(I): 8.17 / Net I/σ(I): 16.4 / Num. measured all: 95174
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.79-1.894.90.451.71360027590.2240.453.299.9
1.89-25.10.2552.91328525970.1240.2555.7100
2-2.145.20.1445.21290124720.070.1449.4100
2.14-2.315.20.098.11185122860.0440.0913.7100
2.31-2.545.20.0759.11105721420.0360.07517.8100
2.54-2.845.10.04913.2991919310.0240.04922.7100
2.84-3.2750.03516.3855517070.0170.03528100
3.27-4.014.80.04412.9713514730.0220.04433.699.6
4.01-5.674.30.03418463510790.0180.03433.993.9
5.67-44.7214.20.02229.322365300.0120.02231.376.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.72 Å
Translation2.5 Å44.72 Å

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3n9b

3n9b


Resolution: 1.793→49.42 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.1838 / FOM work R set: 0.8475 / SU B: 2.571 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1092 / SU Rfree: 0.1057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 974 5.1 %RANDOM
Rwork0.1744 ---
obs0.1759 17965 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 87.83 Å2 / Biso mean: 37.484 Å2 / Biso min: 21.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 1.793→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 33 90 1464
Biso mean--58.89 48.79 -
Num. residues----168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191362
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9851817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1615167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26223.57156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83215239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.018158
X-RAY DIFFRACTIONr_chiral_restr0.1710.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211012
X-RAY DIFFRACTIONr_mcbond_it3.6633.525671
X-RAY DIFFRACTIONr_mcangle_it5.0535.252837
X-RAY DIFFRACTIONr_scbond_it5.0993.859691
LS refinement shellResolution: 1.793→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 74 -
Rwork0.253 1345 -
all-1419 -
obs--99.72 %

+
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