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- PDB-8jc1: Crystal structure of Pectocin M1 from Pectobacterium carotovorum -

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Basic information

Entry
Database: PDB / ID: 8jc1
TitleCrystal structure of Pectocin M1 from Pectobacterium carotovorum
Componentspectocin M1
KeywordsHYDROLASE / bactereocin / pectocin M1 / colicin / ferredoxin-like protein / peptidoglycan
Function / homology
Function and homology information


electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / defense response to bacterium / metal ion binding
Similarity search - Function
Colicin M / Colicin M / Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / SULFITE ION / Ferredoxin (2Fe-2S)
Similarity search - Component
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsJantarit, N. / Kurisu, G. / Tanaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR20E1 Japan
CitationJournal: Febs Open Bio / Year: 2024
Title: Crystal structure of pectocin M1 reveals diverse conformations and interactions during its initial step via the ferredoxin uptake system.
Authors: Jantarit, N. / Tanaka, H. / Lin, Y. / Lee, Y.H. / Kurisu, G.
History
DepositionMay 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pectocin M1
B: pectocin M1
C: pectocin M1
D: pectocin M1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,09829
Polymers117,4184
Non-polymers1,68025
Water9,728540
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13670 Å2
ΔGint-262 kcal/mol
Surface area46130 Å2
Unit cell
Length a, b, c (Å)66.279, 138.553, 68.947
Angle α, β, γ (deg.)90.000, 94.183, 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

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
pectocin M1 / Pectocin M1


Mass: 29354.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Strain: PC1 / Gene: PC1_2303 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: C6DJ69

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Non-polymers , 8 types, 565 molecules

#2: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 19.2% w/v poly(acrylic acid sodium salt) 5,100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.04→49.49 Å / Num. obs: 77569 / % possible obs: 95.5 % / Redundancy: 1.82 % / Biso Wilson estimate: 38.86 Å2 / CC1/2: 0.993 / CC star: 0 / Rmerge(I) obs: 0.077 / Net I/σ(I): 6.63
Reflection shellResolution: 2.04→2.17 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.17 / Num. unique obs: 23492 / CC1/2: 0.7 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9.6model building
PHENIX1.19.2_4158phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N58

4n58


Resolution: 2.04→49.49 Å / SU ML: 0.2753 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.7312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2385 1976 2.55 %
Rwork0.1953 75376 -
obs0.1964 77352 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.94 Å2
Refinement stepCycle: LAST / Resolution: 2.04→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8158 0 67 540 8765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00738368
X-RAY DIFFRACTIONf_angle_d0.847111354
X-RAY DIFFRACTIONf_chiral_restr0.05221256
X-RAY DIFFRACTIONf_plane_restr0.00691492
X-RAY DIFFRACTIONf_dihedral_angle_d6.53691185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.34081110.28824820X-RAY DIFFRACTION87.83
2.09-2.150.28671310.25295427X-RAY DIFFRACTION99.8
2.15-2.210.25291580.22865438X-RAY DIFFRACTION99.86
2.21-2.280.28091350.22285453X-RAY DIFFRACTION99.89
2.28-2.370.28981510.2275421X-RAY DIFFRACTION99.71
2.37-2.460.29811400.2375424X-RAY DIFFRACTION99.93
2.46-2.570.30131450.2385440X-RAY DIFFRACTION99.86
2.57-2.710.29321370.22835446X-RAY DIFFRACTION99.77
2.71-2.880.29031560.21155464X-RAY DIFFRACTION99.82
2.88-3.10.26221400.20715404X-RAY DIFFRACTION99.8
3.1-3.410.27231380.20255455X-RAY DIFFRACTION99.36
3.41-3.910.20881480.1795386X-RAY DIFFRACTION98.54
3.91-4.920.1991430.1535355X-RAY DIFFRACTION97.88
4.92-49.490.18651430.17665443X-RAY DIFFRACTION98.09

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