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- PDB-6vu0: CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF ENZYME I OF THE BAC... -

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Basic information

Entry
Database: PDB / ID: 6vu0
TitleCRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF ENZYME I OF THE BACTERIAL PHOSPHOTRANSFERASE SYSTEM FROM THE ESCHERICHIA COLI ENZYME
ComponentsPEP-protein phosphotransferase system enzyme I
KeywordsTRANSFERASE / phosphoenolpyruvate-protein phosphotransferase PtsI / enzyme I
Function / homology
Function and homology information


phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / N-acetylglucosamine transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. ...Phosphotransferase system, enzyme I / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / : / PEP-utilising enzyme, N-terminal / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Phosphoenolpyruvate-protein phosphotransferase / Phosphoenolpyruvate-protein phosphotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsStewart Jr., C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133488 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Hybrid Thermophilic/Mesophilic Enzymes Reveal a Role for Conformational Disorder in Regulation of Bacterial Enzyme I.
Authors: Dotas, R.R. / Nguyen, T.T. / Stewart Jr., C.E. / Ghirlando, R. / Potoyan, D.A. / Venditti, V.
History
DepositionFeb 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEP-protein phosphotransferase system enzyme I
B: PEP-protein phosphotransferase system enzyme I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8934
Polymers70,7012
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-44 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.460, 136.460, 183.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 261 - 569 / Label seq-ID: 2 - 310

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and resid 261 through 569)AA
2chain 'B'BB

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Components

#1: Protein PEP-protein phosphotransferase system enzyme I


Mass: 35350.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ptsI_2, NCTC9962_06426 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1V2SSS1, UniProt: P08839*PLUS, phosphoenolpyruvate-protein phosphotransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 6.04 Å3/Da / Density % sol: 79.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 500 mM Ammonium sulfate, 1.00 M Lithium sulfate, 100 mM tri-Sodium citrate pH 5.6, 1.0 mM TEW

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2019 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.5→37.07 Å / Num. obs: 54988 / % possible obs: 91.1 % / Redundancy: 5.2 % / Biso Wilson estimate: 94.51 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.45 / Rpim(I) all: 0.164 / Rrim(I) all: 0.483 / Net I/σ(I): 3 / Num. measured all: 285184 / Scaling rejects: 803
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.563.26.4191265440110.0244.1287.6880.291.5
11.18-37.0710.40.07581117800.9970.0240.07920.197.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMv7.2.2data reduction
Aimlessv0.7.3data scaling
PHASERv2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V9K

6v9k


Resolution: 3.5→37.07 Å / SU ML: 0.5006 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.5409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2602 1042 4.96 %
Rwork0.2257 19955 -
obs0.2275 20997 93.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 109.7 Å2
Refinement stepCycle: LAST / Resolution: 3.5→37.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 10 0 4858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00274928
X-RAY DIFFRACTIONf_angle_d0.58366648
X-RAY DIFFRACTIONf_chiral_restr0.0418754
X-RAY DIFFRACTIONf_plane_restr0.004870
X-RAY DIFFRACTIONf_dihedral_angle_d16.02331866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.680.40311330.32182545X-RAY DIFFRACTION85.31
3.68-3.910.35271450.27762546X-RAY DIFFRACTION85.13
3.92-4.220.28911430.23742488X-RAY DIFFRACTION83.92
4.22-4.640.22621640.1942976X-RAY DIFFRACTION98.37
4.64-5.310.22761490.2043053X-RAY DIFFRACTION99.91
5.31-6.680.29851480.24093093X-RAY DIFFRACTION99.94
6.69-37.070.21361600.20693254X-RAY DIFFRACTION99.74

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