[English] 日本語
Yorodumi
- PDB-7pf8: SynFtn Variant E141A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pf8
TitleSynFtn Variant E141A
ComponentsFerritin
KeywordsMETAL BINDING PROTEIN / iron binding protein
Function / homology
Function and homology information


bacterial non-heme ferritin / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
Model detailsstructure determined from crystals of SynFtn D65A that have not been soaked in Fe2+
AuthorsHemmings, A.M. / Bradley, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R002363/1 United Kingdom
CitationJournal: Microbiology (Reading, Engl.) / Year: 2021
Title: Key carboxylate residues for iron transit through the prokaryotic ferritin Syn Ftn.
Authors: Bradley, J.M. / Fair, J. / Hemmings, A.M. / Le Brun, N.E.
History
DepositionAug 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3377
Polymers20,1741
Non-polymers1636
Water3,153175
1
A: Ferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)488,092168
Polymers484,18424
Non-polymers3,909144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_545z,-y-1,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_545-z,-y-1,-x1
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation31_545-z,-x-1/2,y+1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation41_544x,z-1/2,-y-1/21
crystal symmetry operation42_545-x,z-1/2,y+1/21
crystal symmetry operation43_544-x,-z-1/2,-y-1/21
crystal symmetry operation44_545x,-z-1/2,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
crystal symmetry operation82_445-y-1/2,z-1/2,-x1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
crystal symmetry operation85_545y+1/2,x-1/2,-z1
crystal symmetry operation86_445-y-1/2,-x-1/2,-z1
crystal symmetry operation87_545y+1/2,-x-1/2,z1
crystal symmetry operation88_445-y-1/2,x-1/2,z1
Buried area103950 Å2
ΔGint-1276 kcal/mol
Surface area130320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.850, 176.850, 176.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-202-

NA

21A-203-

NA

31A-470-

HOH

41A-474-

HOH

51A-475-

HOH

-
Components

#1: Protein Ferritin


Mass: 20174.320 Da / Num. of mol.: 1 / Fragment: ferritin / Mutation: E141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (strain CC9311) (bacteria)
Strain: CC9311 / Gene: sync_1539 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0I9X8, bacterial non-heme ferritin
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.93 % / Mosaicity: 0 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→62.53 Å / Num. obs: 22172 / % possible obs: 100 % / Redundancy: 77.9 % / Biso Wilson estimate: 39.06 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.011 / Rrim(I) all: 0.094 / Net I/σ(I): 35.4 / Num. measured all: 1726414
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.81-1.86774.10312318616000.8470.4684.131.5100
8.1-62.5361.20.0251978032310.0030.025138.698.5

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 5OUW

5ouw


Resolution: 1.85→40.572 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 1006 4.84 %
Rwork0.1928 19792 -
obs0.194 20798 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.03 Å2 / Biso mean: 34.6776 Å2 / Biso min: 23.38 Å2
Refinement stepCycle: final / Resolution: 1.85→40.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 6 175 1570
Biso mean--51.58 42.6 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071435
X-RAY DIFFRACTIONf_angle_d0.7081954
X-RAY DIFFRACTIONf_chiral_restr0.044219
X-RAY DIFFRACTIONf_plane_restr0.005261
X-RAY DIFFRACTIONf_dihedral_angle_d14.583872
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8502-1.94780.42241350.30962754
1.9478-2.06980.31071370.27632759
2.0698-2.22960.31781540.24292763
2.2296-2.4540.26581370.23052806
2.454-2.8090.25391200.21512821
2.809-3.53870.19711690.18042848
3.5387-40.5720.17361540.16413041

+
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