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- PDB-8yri: Crystal structure of sugar phosphotransferase system EIIB compone... -

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Basic information

Entry
Database: PDB / ID: 8yri
TitleCrystal structure of sugar phosphotransferase system EIIB component CPF_0401 from Clostridium perfringens
ComponentsPTS system, mannose/fructose/sorbose family, IIB component
KeywordsTRANSFERASE / PTS / IIB component
Function / homologyPhosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm / PTS system, mannose/fructose/sorbose family, IIB component
Function and homology information
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHirayama, Y. / Oiki, S. / Mikami, B. / Ogura, K. / Hashimoto, W.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02156 Japan
CitationJournal: To Be Published
Title: Crystal structure of sugar phosphotransferase system EIIB component CPF_0401 from Clostridium perfringens
Authors: Hirayama, Y. / Oiki, S. / Mikami, B. / Ogura, K. / Hashimoto, W.
History
DepositionMar 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTS system, mannose/fructose/sorbose family, IIB component
B: PTS system, mannose/fructose/sorbose family, IIB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2684
Polymers38,0242
Non-polymers2442
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.253, 69.811, 61.863
Angle α, β, γ (deg.)90.000, 90.250, 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

#1: Protein PTS system, mannose/fructose/sorbose family, IIB component / phosphotransferase system EIIB component


Mass: 19012.010 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria)
Gene: CPF_0401 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2YUZ2
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2M magnesium chloride, 0.1M MES (pH6.3), 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→35.25 Å / Num. obs: 23271 / % possible obs: 98 % / Redundancy: 2.64 % / Biso Wilson estimate: 27.66 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.073 / Net I/av σ(I): 10.29 / Net I/σ(I): 10.29
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 2.56 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 3618 / CC1/2: 0.864 / Rrim(I) all: 0.453 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35.25 Å / SU ML: 0.266 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 28.3788
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2573 1162 5 %
Rwork0.2146 22092 -
obs0.2167 23254 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 16 158 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012340
X-RAY DIFFRACTIONf_angle_d1.26443148
X-RAY DIFFRACTIONf_chiral_restr0.0758364
X-RAY DIFFRACTIONf_plane_restr0.0078402
X-RAY DIFFRACTIONf_dihedral_angle_d17.7755916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.33161390.28482653X-RAY DIFFRACTION93.88
1.99-2.090.26741450.2392760X-RAY DIFFRACTION98.78
2.09-2.220.26691470.2182790X-RAY DIFFRACTION99.19
2.22-2.390.27271450.21352766X-RAY DIFFRACTION99.15
2.39-2.630.26651460.22112780X-RAY DIFFRACTION99.25
2.63-3.020.2811470.23852797X-RAY DIFFRACTION98.59
3.02-3.80.27161440.20992723X-RAY DIFFRACTION97.02
3.8-35.250.21711490.19242823X-RAY DIFFRACTION98.02

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