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- PDB-3eye: Crystal structure of PTS system N-acetylgalactosamine-specific II... -

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Basic information

Entry
Database: PDB / ID: 3eye
TitleCrystal structure of PTS system N-acetylgalactosamine-specific IIB component 1 from Escherichia coli
ComponentsPTS system N-acetylgalactosamine-specific IIB component 1
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PHOSPHOTRANSFERASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
Phosphotransferase system, sorbose subfamily IIB component, subgroup / Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetylgalactosamine-specific enzyme IIB component of PTS
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Do, J. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of PTS system N-acetylgalactosamine-specific IIB component 1 from Escherichia coli
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Do, J. / Sampathkumar, P. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS system N-acetylgalactosamine-specific IIB component 1


Theoretical massNumber of molelcules
Total (without water)18,8441
Polymers18,8441
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.878, 31.413, 60.339
Angle α, β, γ (deg.)90.000, 103.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PTS system N-acetylgalactosamine-specific IIB component 1 / EIIB-AGA / Galactosamine-specific PTS system enzyme IIB


Mass: 18844.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: agaB, ECs4018, Z4492 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8XAB8, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 38.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 100mM Tris pH 7.0, 20% PEG 2K, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 18, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.45→58.621 Å / Num. all: 26784 / Num. obs: 26422 / % possible obs: 98.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 10.6
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.3 / Num. measured all: 25454 / Num. unique all: 3833 / Rsym value: 0.422 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.582 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.845 / SU B: 1.397 / SU ML: 0.055 / SU R Cruickshank DPI: 0.075 / SU Rfree: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.075 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1327 5 %RANDOM
Rwork0.19 ---
obs0.192 26409 98.65 %-
all-26770 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 52.72 Å2 / Biso mean: 21.295 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-1.08 Å2
2---0.82 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 0 171 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221236
X-RAY DIFFRACTIONr_bond_other_d0.0020.02832
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9511676
X-RAY DIFFRACTIONr_angle_other_deg1.86332050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70825.26357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81915231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.816157
X-RAY DIFFRACTIONr_chiral_restr0.0980.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021365
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02233
X-RAY DIFFRACTIONr_mcbond_it0.9321.5764
X-RAY DIFFRACTIONr_mcbond_other0.2941.5317
X-RAY DIFFRACTIONr_mcangle_it1.57221253
X-RAY DIFFRACTIONr_scbond_it2.543472
X-RAY DIFFRACTIONr_scangle_it3.9684.5420
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 98 -
Rwork0.255 1832 -
all-1930 -
obs-1832 99.38 %

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