[English] 日本語
Yorodumi
- PDB-1uvh: X-ray structure of Dps from Mycobacterium smegmatis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uvh
TitleX-ray structure of Dps from Mycobacterium smegmatis
ComponentsSTARVATION-INDUCED DNA PROTECTING PROTEIN
KeywordsDNA BINDING PROTEIN / DNA PROTECTION FROM OXIDATIVE DAMAGE
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm
Similarity search - Function
Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA protection during starvation protein / DNA protection during starvation protein
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIlari, A. / Ceci, P. / Falvo, E. / Chiancone, E.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Reassessment of Protein Stability, DNA Binding, and Protection of Mycobacterium Smegmatis Dps.
Authors: Ceci, P. / Ilari, A. / Falvo, E. / Giangiacomo, L. / Chiancone, E.
History
DepositionJan 20, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STARVATION-INDUCED DNA PROTECTING PROTEIN
B: STARVATION-INDUCED DNA PROTECTING PROTEIN
C: STARVATION-INDUCED DNA PROTECTING PROTEIN
D: STARVATION-INDUCED DNA PROTECTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4198
Polymers81,1954
Non-polymers2234
Water82946
1
A: STARVATION-INDUCED DNA PROTECTING PROTEIN
B: STARVATION-INDUCED DNA PROTECTING PROTEIN
C: STARVATION-INDUCED DNA PROTECTING PROTEIN
D: STARVATION-INDUCED DNA PROTECTING PROTEIN
hetero molecules

A: STARVATION-INDUCED DNA PROTECTING PROTEIN
B: STARVATION-INDUCED DNA PROTECTING PROTEIN
C: STARVATION-INDUCED DNA PROTECTING PROTEIN
D: STARVATION-INDUCED DNA PROTECTING PROTEIN
hetero molecules

A: STARVATION-INDUCED DNA PROTECTING PROTEIN
B: STARVATION-INDUCED DNA PROTECTING PROTEIN
C: STARVATION-INDUCED DNA PROTECTING PROTEIN
D: STARVATION-INDUCED DNA PROTECTING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,25624
Polymers243,58612
Non-polymers67012
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.300, 124.300, 304.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.00051, 0.57675, -0.81692), (0.57746, -0.66678, -0.4711), (-0.81642, -0.47198, -0.33271)1.33474, 1.66684, 0.66645
2given(0.49915, 0.86652, 7.0E-5), (0.2895, -0.16685, 0.94252), (0.81672, -0.47044, -0.33414)-0.66688, -0.33358, 0.66662
3given(0.50106, -0.28748, -0.81627), (-0.86541, -0.16848, -0.47188), (-0.00187, 0.94285, -0.33321)1.667, 1.33518, 0.3335

-
Components

#1: Protein
STARVATION-INDUCED DNA PROTECTING PROTEIN / DPS


Mass: 20298.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VP75, UniProt: P0C558*PLUS
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.5
Details: HEPES 0.1 M, IN A PH RANGE BETWEEN 7.0-7.8. AMMONIUM SULFATE IN A RANGE BETWEEN 1.5-2.0 M

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorDate: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 22346 / % possible obs: 99 % / Redundancy: 10 % / Rmerge(I) obs: 0.082

-
Processing

Software
NameClassification
REFMACrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPS

1dps


Resolution: 2.8→40 Å / Cross valid method: THROUGHOUT
Details: COORDINATES FOR A COMPLETE DODECAMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING CRYSTALLOGRAPHIC SYMMETRY OPERATIONS ...Details: COORDINATES FOR A COMPLETE DODECAMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING CRYSTALLOGRAPHIC SYMMETRY OPERATIONS GIVEN BELOW TO THE TETRAMER OF THE ASYMMETRIC UNIT: SYMGEN X,Y,Z SYMGEN Y-X, 1-X,Z SYMGEN 1-Y,1+X-Y,Z
RfactorNum. reflection% reflectionSelection details
Rfree0.34 1117 5 %RANDOM
Rwork0.26 ---
obs0.27 21227 99 %-
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4928 0 4 46 4978

+
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