[English] 日本語
Yorodumi
- PDB-21zf: Crystal structure of the petrobactin-binding protein FatB from Ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 21zf
TitleCrystal structure of the petrobactin-binding protein FatB from Bacillus cereus complexed with ferric petrobactin photoproduct, FePBv
ComponentsFerric anguibactin-binding protein
KeywordsMETAL TRANSPORT PROTEIN / siderophore-binding protein / substrate-binding protein / ABC transporter
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space / plasma membrane
Similarity search - Function
FatB domain / : / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / : / Ferric anguibactin-binding protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLee, H. / Kim, S.O. / You, S. / Noh, T. / Ihee, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Institute for Basic Science (IBS)IBS-R033 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of FatB-mediated iron uptake via tyrosine/histidine direct coordination accompanying long-distance domain reorganization.
Authors: Lee, H. / Kim, S.O. / You, S. / Segalina, A. / Noh, T. / Ihee, H.
History
DepositionJan 4, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferric anguibactin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4693
Polymers32,7401
Non-polymers7292
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration (Size-exclusion) chromatography showed a single major peak consistent with a monomeric species in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.563, 66.483, 50.114
Angle α, β, γ (deg.)90.000, 91.700, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Ferric anguibactin-binding protein / Petrobactin-binding protein FatB


Mass: 32739.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct corresponds to residues 40-338 of Bacillus cereus FatB (UniProt Q815N5). Three additional residues, Ser-Asn-Ala (SNA), are present at the N-terminus as a remnant of the His6- ...Details: The construct corresponds to residues 40-338 of Bacillus cereus FatB (UniProt Q815N5). Three additional residues, Ser-Asn-Ala (SNA), are present at the N-terminus as a remnant of the His6-tag following TEV protease cleavage.
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_5106 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q815N5
#2: Chemical ChemComp-A1MDH / ~{N}-[3-[4-[[5-[4-[3-[[3,4-bis(oxidanyl)phenyl]carbonylamino]propylamino]butylamino]-5-oxidanyl-3-oxidanylidene-pent-4-enoyl]amino]butylamino]propyl]-3,4-bis(oxidanyl)benzamide


Mass: 672.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H48N6O9 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10% (v/v) 2-propanol, 0.1 M BICINE, pH 8.5, 28% (w/v) PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2026
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.58→40.01 Å / Num. obs: 34799 / % possible obs: 97.69 % / Redundancy: 4 % / Biso Wilson estimate: 12.84 Å2 / CC1/2: 0.987 / CC star: 0.997 / Net I/σ(I): 14.15
Reflection shellResolution: 1.582→1.639 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3320 / CC1/2: 0.937 / CC star: 0.984

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000v722data reduction
HKL-2000v722data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→40.01 Å / SU ML: 0.1409 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.9107
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1882 2014 5.82 %
Rwork0.1553 32592 -
obs0.1572 34606 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.86 Å2
Refinement stepCycle: LAST / Resolution: 1.58→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 49 393 2695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00582383
X-RAY DIFFRACTIONf_angle_d0.81263237
X-RAY DIFFRACTIONf_chiral_restr0.0539364
X-RAY DIFFRACTIONf_plane_restr0.0061422
X-RAY DIFFRACTIONf_dihedral_angle_d14.7938892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.620.23861430.17512190X-RAY DIFFRACTION93.88
1.62-1.670.20851380.16162355X-RAY DIFFRACTION98.19
1.67-1.710.2051480.16022326X-RAY DIFFRACTION98.49
1.71-1.770.21121440.17322305X-RAY DIFFRACTION97.84
1.77-1.830.21761320.16382261X-RAY DIFFRACTION95.61
1.83-1.910.19861450.15832388X-RAY DIFFRACTION98.91
1.91-1.990.20631430.15462360X-RAY DIFFRACTION99.21
1.99-2.10.17581530.15132349X-RAY DIFFRACTION98.85
2.1-2.230.1851370.15492262X-RAY DIFFRACTION95.46
2.23-2.40.18651470.16142380X-RAY DIFFRACTION99.53
2.4-2.640.19511460.1672370X-RAY DIFFRACTION99.21
2.64-3.030.21821360.16662332X-RAY DIFFRACTION97.51
3.03-3.810.17561490.14742369X-RAY DIFFRACTION98.82
3.81-40.010.15761530.1382345X-RAY DIFFRACTION96.11

+
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