[English] 日本語
Yorodumi
- PDB-9nhr: Crystal structure of structure of WT BfrB from Pseudomonas aerugi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nhr
TitleCrystal structure of structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor KM-5-25
ComponentsFerroxidase
KeywordsOXIDOREDUCTASE / biofilms / electron transport / iron storage / iron binding / iron mobilization / protein-protein interaction inhibitor
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / iron ion binding / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / 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
: / PROTOPORPHYRIN IX CONTAINING FE / : / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLovell, S. / Seibold, S. / Battaile, K.P. / Yao, H. / Rivera, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10 OD030394 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI169344 United States
CitationJournal: Acs Infect Dis. / Year: 2025
Title: Inhibitors of the Bacterioferritin Ferredoxin Complex Dysregulate Iron Homeostasis and Kill Acinetobacter baumannii and Biofilm-Embedded Pseudomonas aeruginosa Cells.
Authors: Behm, A.M. / Yao, H. / Eze, E.C. / Alli, S.A. / Baugh, S.D.P. / Ametsetor, E. / Powell, K.M. / Battaile, K.P. / Seibold, S. / Lovell, S. / Bunce, R.A. / Reitz, A.B. / Rivera, M.
History
DepositionFeb 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)231,67339
Polymers222,96212
Non-polymers8,71127
Water12,520695
1
A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)463,34678
Polymers445,92424
Non-polymers17,42254
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area98610 Å2
ΔGint-581 kcal/mol
Surface area121670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.569, 194.357, 203.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11D-202-

HEM

21D-202-

HEM

31D-202-

HEM

41L-201-

HEM

51L-201-

HEM

61L-201-

HEM

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Ferroxidase


Mass: 18580.168 Da / Num. of mol.: 12 / Fragment: BFRB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: bfrB, PA3531 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase

-
Non-polymers , 5 types, 722 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-A1BYB / 4-{[(5-chloro-2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione


Mass: 302.712 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C15H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% v/v PEG200, 100 mM sodium acetate, pH 4.5, 100 mM sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 3, 2021
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.59 Å / Num. obs: 185210 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Χ2: 1.04 / Net I/σ(I): 12.5 / Num. measured all: 1284414
Reflection shellResolution: 1.95→1.98 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 1.043 / Num. measured all: 61051 / Num. unique obs: 9123 / CC1/2: 0.746 / Rpim(I) all: 0.435 / Rrim(I) all: 1.131 / Χ2: 1.03 / Net I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
PHENIX(dev_4210: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→38 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 9277 5.01 %
Rwork0.1798 --
obs0.1819 185107 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15173 0 590 695 16458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116194
X-RAY DIFFRACTIONf_angle_d0.92621954
X-RAY DIFFRACTIONf_dihedral_angle_d15.4365978
X-RAY DIFFRACTIONf_chiral_restr0.0462348
X-RAY DIFFRACTIONf_plane_restr0.0082780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.30393140.26745807X-RAY DIFFRACTION100
1.97-20.29552910.25295830X-RAY DIFFRACTION100
2-2.020.30473230.24565820X-RAY DIFFRACTION100
2.02-2.050.26583270.22965758X-RAY DIFFRACTION100
2.05-2.070.25152850.21875817X-RAY DIFFRACTION100
2.07-2.10.24843060.21145816X-RAY DIFFRACTION100
2.1-2.130.27923230.20685855X-RAY DIFFRACTION100
2.13-2.160.25532990.20885852X-RAY DIFFRACTION100
2.16-2.20.26043070.19385784X-RAY DIFFRACTION100
2.2-2.230.22652980.18435852X-RAY DIFFRACTION100
2.23-2.270.23183300.18475811X-RAY DIFFRACTION100
2.27-2.310.22872940.17785825X-RAY DIFFRACTION100
2.31-2.360.2432970.18215849X-RAY DIFFRACTION100
2.36-2.40.24753100.18135834X-RAY DIFFRACTION100
2.4-2.460.22032980.17575843X-RAY DIFFRACTION100
2.46-2.510.21292870.1725843X-RAY DIFFRACTION100
2.51-2.580.21713580.16965814X-RAY DIFFRACTION100
2.58-2.650.21082880.16695882X-RAY DIFFRACTION100
2.65-2.720.23193220.17955845X-RAY DIFFRACTION100
2.72-2.810.23432970.17055845X-RAY DIFFRACTION100
2.81-2.910.20453090.16235848X-RAY DIFFRACTION100
2.91-3.030.21662660.17585892X-RAY DIFFRACTION100
3.03-3.170.23563350.18595885X-RAY DIFFRACTION100
3.17-3.330.2343040.18715887X-RAY DIFFRACTION100
3.33-3.540.20933020.17325885X-RAY DIFFRACTION100
3.54-3.820.20073280.17315878X-RAY DIFFRACTION100
3.82-4.20.20163150.15645904X-RAY DIFFRACTION100
4.2-4.810.16623160.14485941X-RAY DIFFRACTION100
4.81-6.050.2353250.19095975X-RAY DIFFRACTION100
6.05-380.21893230.19636153X-RAY DIFFRACTION100

+
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