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- PDB-9p4s: HmuS heme dechelatase: disordered domain 1, heme free. -

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Basic information

Entry
Database: PDB / ID: 9p4s
TitleHmuS heme dechelatase: disordered domain 1, heme free.
ComponentsHmuS heme dechelatase
KeywordsMETAL TRANSPORT / Iron / Microbiome / Heme
Function / homologycobaltochelatase activity / CobN/magnesium chelatase / CobN/Magnesium Chelatase / biosynthetic process / membrane / Cobaltochelatase subunit CobN
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsGauvin, C.C. / Nath, A.K. / Rodrigues da Silva, R. / Akpoto, E. / Dubois, J.L. / Lawrence, C.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Science Foundation (NSF, United States)DBI-1828765 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM140963 United States
CitationJournal: To Be Published
Title: HmuS Heme Dechelatase: Disordered Domain 1, Heme Free
Authors: Nath, A.K. / Rodrigues da Silva, R. / Gauvin, C.C. / Akpoto, E. / Lawrence, C.M. / Dubois, J.L.
History
DepositionJun 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HmuS heme dechelatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,4693
Polymers162,4231
Non-polymers462
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein HmuS heme dechelatase


Mass: 162423.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: GAN91_17490, GAO51_10745, KQP68_24275 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0FP54
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HmuS in complex with heme / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.153058 MDa / Experimental value: NO
Source (natural)Organism: Bacteroides thetaiotaomicron (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.1
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-ClC4H11NO3Cl1
2250 mMSodium ChlorideNaCl1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 55187 X / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.06 sec. / Electron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12602

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2SerialEMimage acquisition
4cryoSPARC4CTF correction
7PHENIX1.20.1model fitting
9PHENIX1.20.1model refinement
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
12cryoSPARC4classification
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 18955798 / Details: Blob picked, then particles washed to give
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3795134 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 119.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00238990
ELECTRON MICROSCOPYf_angle_d0.437812170
ELECTRON MICROSCOPYf_chiral_restr0.03881323
ELECTRON MICROSCOPYf_plane_restr0.00381596
ELECTRON MICROSCOPYf_dihedral_angle_d11.02373359

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