[English] 日本語
Yorodumi
- PDB-4u3g: Crystal structure of Escherichia coli bacterioferritin mutant D132F -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u3g
TitleCrystal structure of Escherichia coli bacterioferritin mutant D132F
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / iron channel / 4-helix bundle / diiron site
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis
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
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsWong, S.G. / Grigg, J.C. / Le Brun, N.E. / Moore, G.R. / Murphy, M.E.P. / Mauk, A.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
CIHR/Canadian Blood Services Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The B-type Channel Is a Major Route for Iron Entry into the Ferroxidase Center and Central Cavity of Bacterioferritin.
Authors: Wong, S.G. / Grigg, J.C. / Le Brun, N.E. / Moore, G.R. / Murphy, M.E. / Mauk, A.G.
History
DepositionJul 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.4Sep 27, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,13828
Polymers222,60112
Non-polymers1,53716
Water60,1163337
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)448,27656
Polymers445,20224
Non-polymers3,07432
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area82060 Å2
ΔGint-729 kcal/mol
Surface area137200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.518, 208.518, 142.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-309-

HOH

21B-319-

HOH

31L-314-

HOH

41L-315-

HOH

51L-334-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid C
41chain D and segid D
51chain E and segid E
61chain F and segid F
71chain G and segid G
81chain H and segid H
91chain I and segid I
101chain J and segid J
111chain K and segid K
121chain L and segid L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid CC0
411chain D and segid DD0
511chain E and segid EE0
611chain F and segid FF0
711chain G and segid GG0
811chain H and segid HH0
911chain I and segid II0
1011chain J and segid JJ0
1111chain K and segid KK0
1211chain L and segid LL0

-
Components

#1: Protein
Bacterioferritin / BFR / Cytochrome b-1 / Cytochrome b-557


Mass: 18550.102 Da / Num. of mol.: 12 / Mutation: D132F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:H1 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC / Gene: bfr, c4107 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABD4, ferroxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3337 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate (50-80% saturated), NaCl (0.1 M), and TrisHCl (20 mM, pH 7.2)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.15 Å / Num. obs: 209838 / % possible obs: 99.7 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.056 / Net I/σ(I): 11.2 / Num. measured all: 1024612
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.033.80.6352.138570102730.8680.37499.4
10.95-49.156.70.023389693145510.0198.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata scaling
Aimlessdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y3Q

2y3q


Resolution: 2→49.148 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 10307 4.93 %
Rwork0.1901 384359 -
obs0.1916 209745 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.68 Å2 / Biso mean: 15.8113 Å2 / Biso min: 1.13 Å2
Refinement stepCycle: final / Resolution: 2→49.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15612 0 80 3337 19029
Biso mean--38.66 30.06 -
Num. residues----1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716216
X-RAY DIFFRACTIONf_angle_d0.89721888
X-RAY DIFFRACTIONf_chiral_restr0.042340
X-RAY DIFFRACTIONf_plane_restr0.0042880
X-RAY DIFFRACTIONf_dihedral_angle_d12.9616288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9348X-RAY DIFFRACTION5.334TORSIONAL
12B9348X-RAY DIFFRACTION5.334TORSIONAL
13C9348X-RAY DIFFRACTION5.334TORSIONAL
14D9348X-RAY DIFFRACTION5.334TORSIONAL
15E9348X-RAY DIFFRACTION5.334TORSIONAL
16F9348X-RAY DIFFRACTION5.334TORSIONAL
17G9348X-RAY DIFFRACTION5.334TORSIONAL
18H9348X-RAY DIFFRACTION5.334TORSIONAL
19I9348X-RAY DIFFRACTION5.334TORSIONAL
110J9348X-RAY DIFFRACTION5.334TORSIONAL
111K9348X-RAY DIFFRACTION5.334TORSIONAL
112L9348X-RAY DIFFRACTION5.334TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02270.31216450.295129521359799
2.0227-2.04650.31576700.2865127131338399
2.0465-2.07150.34246810.2851127231340499
2.0715-2.09770.29936820.2747126571333999
2.0977-2.12530.2787240.23751280113525100
2.1253-2.15440.26226960.2329127551345199
2.1544-2.18520.25636270.22321293213559100
2.1852-2.21780.236500.21941289513545100
2.2178-2.25250.26396570.2401125851324298
2.2525-2.28940.26336220.2243128301345299
2.2894-2.32890.23656250.21141284013465100
2.3289-2.37120.24456890.21681285813547100
2.3712-2.41680.22617230.20411281213535100
2.4168-2.46620.25167140.20131281513529100
2.4662-2.51980.24686700.19791286913539100
2.5198-2.57840.23257130.19451282813541100
2.5784-2.64290.24586770.19281279413471100
2.6429-2.71430.23226620.197127761343899
2.7143-2.79420.21516740.1831127941346899
2.7942-2.88440.21466710.17021282413495100
2.8844-2.98740.1835940.16751295613550100
2.9874-3.1070.18796470.17261290813555100
3.107-3.24840.18867030.15621282313526100
3.2484-3.41960.17877010.1461282713528100
3.4196-3.63380.17616700.14251275813428100
3.6338-3.91430.16666080.14171292713535100
3.9143-4.3080.15946380.1298128661350499
4.308-4.93090.15736800.13971282513505100
4.9309-6.21040.2016430.19451289213535100
6.2104-49.1630.19735990.1796125241312397

+
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