[English] 日本語
Yorodumi
- PDB-1qgh: THE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LIST... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qgh
TitleTHE X-RAY STRUCTURE OF THE UNUSUAL DODECAMERIC FERRITIN FROM LISTERIA INNOCUA, REVEALS A NOVEL INTERSUBUNIT IRON BINDING SITE.
ComponentsNON-HEME IRON-CONTAINING FERRITIN
KeywordsMETAL TRANSPORT / FERRITIN
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Dps protein family signature 2. / 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 ...Dps protein family signature 2. / 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
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsIlari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site.
Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
History
DepositionApr 27, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_struct_conn_angle.value / _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 / _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: NON-HEME IRON-CONTAINING FERRITIN
B: NON-HEME IRON-CONTAINING FERRITIN
C: NON-HEME IRON-CONTAINING FERRITIN
D: NON-HEME IRON-CONTAINING FERRITIN
E: NON-HEME IRON-CONTAINING FERRITIN
F: NON-HEME IRON-CONTAINING FERRITIN
G: NON-HEME IRON-CONTAINING FERRITIN
H: NON-HEME IRON-CONTAINING FERRITIN
I: NON-HEME IRON-CONTAINING FERRITIN
J: NON-HEME IRON-CONTAINING FERRITIN
K: NON-HEME IRON-CONTAINING FERRITIN
L: NON-HEME IRON-CONTAINING FERRITIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,51724
Polymers216,84712
Non-polymers67012
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38490 Å2
ΔGint-369 kcal/mol
Surface area60820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.540, 137.500, 173.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.02534, -0.00322, -0.99967), (-0.00289, -0.99999, 0.00315), (-0.99967, 0.00281, -0.0253)30.92601, 0.14676, 31.67621
2given(-0.56524, -0.69426, 0.44554), (-0.69392, 0.10811, -0.71189), (0.44607, -0.71156, -0.54287)16.93955, 22.19773, 17.90978
3given(-0.45944, 0.69427, 0.55399), (0.69698, -0.10482, 0.70939), (0.55058, 0.71204, -0.43573)13.46489, -21.91316, 14.38429
4given(-0.20491, 0.21849, -0.95408), (0.86458, 0.49734, -0.0718), (0.45882, -0.83959, -0.29081)33.73081, -11.88506, 13.68209
5given(0.94931, -0.21652, 0.22787), (0.09265, -0.49997, -0.86107), (0.30037, 0.83854, -0.45457)-2.64692, 12.34241, 18.55365
6given(-0.46544, 0.84452, 0.26487), (-0.86353, -0.49893, 0.07336), (0.1941, -0.19458, 0.96149)18.20738, 12.1298, -2.29897
7given(-0.27795, -0.84229, 0.46184), (-0.09476, 0.50248, 0.85938), (-0.95591, 0.1951, -0.21948)12.36059, -12.03838, 33.96724
8given(-0.20941, 0.86728, 0.45163), (0.21646, 0.49152, -0.84353), (-0.95357, -0.07889, -0.29066)11.43735, 10.10695, 34.9837
9given(-0.4642, -0.86409, 0.19457), (0.84394, -0.49818, -0.19896), (0.26886, 0.07185, 0.9605)19.50842, -9.60517, -3.5069
10given(-0.28023, -0.09486, -0.95523), (-0.84316, 0.49999, 0.1977), (0.45885, 0.86082, -0.2201)34.7996, 9.82864, 12.27548
11given(0.94789, 0.09683, 0.30353), (-0.21849, -0.49583, 0.84048), (0.23189, -0.863, -0.44883)-3.86911, -9.90294, 19.56981

-
Components

#1: Protein
NON-HEME IRON-CONTAINING FERRITIN


Mass: 18070.553 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Listeria innocua (bacteria) / References: UniProt: P80725
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growpH: 5.8
Details: PEG 1000 AT 19-25 %, MES 0.1 M AT PH 5.0-6.2, pH 5.8
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
20.1 MMES1reservoir
319-25 %PEG10001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8373
DetectorDate: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8373 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 80150 / % possible obs: 91.3 % / Redundancy: 3.8 % / Rsym value: 0.077
Reflection
*PLUS
Rmerge(I) obs: 0.077

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPS

1dps


Resolution: 2.35→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.219 --
all0.219 --
obs-80098 91 %
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14664 0 12 479 15155
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.039
X-RAY DIFFRACTIONt_dihedral_angle_d14.698
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.011
X-RAY DIFFRACTIONt_gen_planes0.016
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.698
X-RAY DIFFRACTIONt_plane_restr0.016

+
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