[English] 日本語
Yorodumi
- PDB-5mll: Structure of HpDprA at 1.9 Angstroms resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mll
TitleStructure of HpDprA at 1.9 Angstroms resolution
ComponentsDNA processing chain A (DprA)
KeywordsDNA BINDING PROTEIN / HpDprA
Function / homologyDNA recombination-mediator protein A / DNA recombination-mediator protein A / DNA-mediated transformation / Rossmann fold - #450 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DNA processing chain A (DprA)
Function and homology information
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLisboa, J. / Quevillon-Cheruel, S.
CitationJournal: FEBS J. / Year: 2019
Title: The C-terminal domain of HpDprA is a DNA-binding Winged Helix domain that does not bind double-stranded DNA.
Authors: Lisboa, J. / Celma, L. / Sanchez, D. / Marquis, M. / Andreani, J. / Guerois, R. / Ochsenbein, F. / Durand, D. / Marsin, S. / Cuniasse, P. / Radicella, J.P. / Quevillon-Cheruel, S.
History
DepositionDec 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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: DNA processing chain A (DprA)
B: DNA processing chain A (DprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0875
Polymers48,9012
Non-polymers1863
Water2,594144
1
A: DNA processing chain A (DprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5753
Polymers24,4501
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA processing chain A (DprA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5122
Polymers24,4501
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.380, 67.580, 159.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA processing chain A (DprA)


Mass: 24450.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_0333 / Production host: Escherichia coli (E. coli) / References: UniProt: O25100
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 200mM di-ammonium tartrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 35234 / % possible obs: 99.4 % / Redundancy: 4.35 % / Biso Wilson estimate: 29.3 Å2 / Net I/σ(I): 3.2
Reflection shellResolution: 1.9→1.966 Å / Redundancy: 4.35 % / % possible all: 96.98

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UQZ

3uqz


Resolution: 1.9→41.753 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.05
RfactorNum. reflection% reflection
Rfree0.2472 1760 5 %
Rwork0.1953 --
obs0.1979 35196 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3418 0 12 144 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073517
X-RAY DIFFRACTIONf_angle_d14758
X-RAY DIFFRACTIONf_dihedral_angle_d13.3581353
X-RAY DIFFRACTIONf_chiral_restr0.041553
X-RAY DIFFRACTIONf_plane_restr0.005611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8986-1.950.35571290.27032449X-RAY DIFFRACTION96
1.95-2.00730.26461330.24342515X-RAY DIFFRACTION99
2.0073-2.07210.27921320.22352530X-RAY DIFFRACTION100
2.0721-2.14620.27421330.21712538X-RAY DIFFRACTION100
2.1462-2.23210.30491340.20732554X-RAY DIFFRACTION100
2.2321-2.33370.26631350.21382562X-RAY DIFFRACTION100
2.3337-2.45670.28321340.22032542X-RAY DIFFRACTION100
2.4567-2.61060.26461360.21342570X-RAY DIFFRACTION100
2.6106-2.81210.26451350.21742574X-RAY DIFFRACTION100
2.8121-3.0950.26741370.21532594X-RAY DIFFRACTION100
3.095-3.54270.25961370.20052597X-RAY DIFFRACTION100
3.5427-4.46260.21271390.16472645X-RAY DIFFRACTION100
4.4626-41.76320.20061460.16222766X-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