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- PDB-9b86: FetB apo from Porphyromonas gingivalis without heme group -

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Basic information

Entry
Database: PDB / ID: 9b86
TitleFetB apo from Porphyromonas gingivalis without heme group
ComponentsHeme-binding protein FetB
KeywordsOXYGEN STORAGE / FetB / heme / metal binding / apo
Function / homologyAnaerobic cobalt chelatase / Cobalt chelatase (CbiK) / sirohydrochlorin cobaltochelatase activity / anaerobic cobalamin biosynthetic process / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / Heme-binding protein FetB
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAtaide, S.F. / Kwan, A. / Phonok, Y. / Gao, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: FetB apo from Porphyromonas gingivalis without heme group
Authors: Ataide, S.F. / Kwan, A. / Phonok, Y. / Gao, J.
History
DepositionMar 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-binding protein FetB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9687
Polymers32,7541
Non-polymers2146
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.631, 49.817, 98.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heme-binding protein FetB


Mass: 32754.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: fetB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RMI6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 150 mM MgCl2 24% PEG4000 Bis-Tris pH 6.4

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.94644 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94644 Å / Relative weight: 1
ReflectionResolution: 1.6→48.63 Å / Num. obs: 32713 / % possible obs: 99.8 % / Redundancy: 3 % / CC1/2: 1 / Net I/σ(I): 19.8
Reflection shellResolution: 1.6→3.44 Å / Num. unique obs: 32654 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→34.8 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 1593 4.88 %
Rwork0.2024 --
obs0.2036 32648 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→34.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 11 181 2242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072093
X-RAY DIFFRACTIONf_angle_d0.8892825
X-RAY DIFFRACTIONf_dihedral_angle_d6.195282
X-RAY DIFFRACTIONf_chiral_restr0.054316
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.29921350.27282740X-RAY DIFFRACTION98
1.65-1.710.3031530.27272781X-RAY DIFFRACTION100
1.71-1.770.3181460.27962768X-RAY DIFFRACTION100
1.77-1.860.3061330.24912803X-RAY DIFFRACTION100
1.86-1.950.29141480.23112793X-RAY DIFFRACTION100
1.95-2.080.24871230.22622816X-RAY DIFFRACTION100
2.08-2.240.26021390.21742819X-RAY DIFFRACTION100
2.24-2.460.24341370.21112837X-RAY DIFFRACTION100
2.46-2.820.23771520.21212832X-RAY DIFFRACTION100
2.82-3.550.23211600.18872871X-RAY DIFFRACTION100
3.55-34.80.17281670.17152995X-RAY DIFFRACTION100

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