[English] 日本語
Yorodumi
- PDB-5xx9: Crystal structure of Bacterioferritin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xx9
TitleCrystal structure of Bacterioferritin
ComponentsBacterioferritin
KeywordsMETAL TRANSPORT / Bacterioferritin
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Bacterioferritin
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJobichen, C. / Rajesh, R. / Angayarkanni, J. / Sivaraman, J.
CitationJournal: Pnas Nexus / Year: 2023
Title: Bacterioferritin nanocage structures uncover the bio-mineralization process in ferritins
Authors: Jobichen, C. / Chong, T.Y. / Rattinam, R. / Basak, S. / Srinivasan, M. / Choong, Y.K. / Pandey, K.P. / Ngoc, T.B. / Shi, J. / Angayarkanni, J. / Sivaraman, J.
History
DepositionJul 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
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.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_symmetry
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,12618
Polymers115,4566
Non-polymers67012
Water11,259625
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
F: Bacterioferritin
hetero molecules

E: Bacterioferritin
hetero molecules

E: Bacterioferritin
hetero molecules

E: Bacterioferritin
hetero molecules

E: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,50472
Polymers461,82324
Non-polymers2,68148
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_445x-1/2,y-1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_545-y+1/2,x-1/2,z+1/21
crystal symmetry operation8_455y-1/2,-x+1/2,z+1/21
Buried area87190 Å2
ΔGint-997 kcal/mol
Surface area129090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.761, 123.761, 172.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein
Bacterioferritin / BFR


Mass: 19242.629 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: bfr, SCO2113, SC6E10.07 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S2N0, ferroxidase
#2: Chemical
ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 3000, 0.1M HEPES pH 7.5, 0.2M NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→43.8 Å / Num. obs: 76305 / % possible obs: 97 % / Redundancy: 5 % / Net I/σ(I): 3.1

-
Processing

Software
NameVersionClassification
PHENIX(dev_2733)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CVT

4cvt


Resolution: 2.6→43.756 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2084 3875 5.08 %
Rwork0.1605 --
obs0.1629 76305 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→43.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7817 0 12 625 8454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077947
X-RAY DIFFRACTIONf_angle_d0.89910740
X-RAY DIFFRACTIONf_dihedral_angle_d4.4254824
X-RAY DIFFRACTIONf_chiral_restr0.0491220
X-RAY DIFFRACTIONf_plane_restr0.0061402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5997-2.63140.2391130.19631946X-RAY DIFFRACTION72
2.6314-2.66470.22031230.19462056X-RAY DIFFRACTION79
2.6647-2.69980.24361120.19462269X-RAY DIFFRACTION85
2.6998-2.73670.25031170.1872444X-RAY DIFFRACTION90
2.7367-2.77580.21891280.18112478X-RAY DIFFRACTION93
2.7758-2.81730.21621610.18012623X-RAY DIFFRACTION98
2.8173-2.86130.24481460.17792604X-RAY DIFFRACTION100
2.8613-2.90820.25141440.17962660X-RAY DIFFRACTION100
2.9082-2.95830.21711640.16572654X-RAY DIFFRACTION100
2.9583-3.01210.20891420.1752696X-RAY DIFFRACTION100
3.0121-3.070.24361460.16682689X-RAY DIFFRACTION100
3.07-3.13270.21471320.17722636X-RAY DIFFRACTION100
3.1327-3.20080.2771180.17582647X-RAY DIFFRACTION100
3.2008-3.27520.23621400.16882693X-RAY DIFFRACTION100
3.2752-3.35710.22611280.17092673X-RAY DIFFRACTION100
3.3571-3.44780.21921520.17232699X-RAY DIFFRACTION100
3.4478-3.54920.22491390.15812662X-RAY DIFFRACTION100
3.5492-3.66370.20251320.14412632X-RAY DIFFRACTION100
3.6637-3.79460.16471360.14462690X-RAY DIFFRACTION100
3.7946-3.94640.16791500.14972680X-RAY DIFFRACTION100
3.9464-4.12590.21571300.13992686X-RAY DIFFRACTION100
4.1259-4.34320.19041480.13252659X-RAY DIFFRACTION100
4.3432-4.61510.17081280.1272667X-RAY DIFFRACTION100
4.6151-4.9710.22651640.15112652X-RAY DIFFRACTION100
4.971-5.47040.21341440.15662657X-RAY DIFFRACTION100
5.4704-6.260.21791380.18072684X-RAY DIFFRACTION100
6.26-7.87940.1741540.16272656X-RAY DIFFRACTION100
7.8794-43.76230.15541460.14792654X-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://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