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- PDB-6bvg: Crystal structure of bcMalT T280C-E54C crosslinked by divalent mercury -

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Basic information

Entry
Database: PDB / ID: 6bvg
TitleCrystal structure of bcMalT T280C-E54C crosslinked by divalent mercury
ComponentsProtein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
KeywordsTRANSPORT PROTEIN / EIIC maltose transporter
Function / homology
Function and homology information


protein-Npi-phosphohistidine-sugar phosphotransferase / protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / plasma membrane
Similarity search - Function
Phosphotransferase system, IIBC component / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC
Similarity search - Domain/homology
alpha-maltose / : / Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRen, Z. / Zhou, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087519 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of an EIIC sugar transporter trapped in an inward-facing conformation.
Authors: Ren, Z. / Lee, J. / Moosa, M.M. / Nian, Y. / Hu, L. / Xu, Z. / McCoy, J.G. / Ferreon, A.C.M. / Im, W. / Zhou, M.
History
DepositionDec 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / refine_hist / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _refine_hist.d_res_low / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
B: Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7276
Polymers97,6412
Non-polymers1,0864
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-96 kcal/mol
Surface area36250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.818, 114.367, 196.987
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 Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)


Mass: 48820.465 Da / Num. of mol.: 2 / Fragment: residues 3-451 / Mutation: T280C, E54C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ZK / E33L) (bacteria)
Strain: ZK / E33L / Gene: ptsG, BCE33L0344 / Plasmid: pMCSG28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q63GK8, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg

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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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Glycine, pH 8.8-9.1, 33-38% PEG 400, 50 mM CoCl2 and 10-20 mM spermine tetrahydrochloride
PH range: 8.8-9.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3.2→29.42 Å / Num. obs: 24635 / % possible obs: 96.76 % / Redundancy: 4.5 % / Biso Wilson estimate: 37.47 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.058 / Rrim(I) all: 0.13 / Χ2: 0.998 / Net I/σ(I): 12.16
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2330 / CC1/2: 0.817 / Rpim(I) all: 0.384 / Rrim(I) all: 0.85 / Χ2: 0.884 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IWS

5iws


Resolution: 3.2→29.42 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2918 1319 5.38 %
Rwork0.2514 --
obs0.2536 24635 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6862 0 48 0 6910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037082
X-RAY DIFFRACTIONf_angle_d0.6099642
X-RAY DIFFRACTIONf_dihedral_angle_d2.3964078
X-RAY DIFFRACTIONf_chiral_restr0.0431144
X-RAY DIFFRACTIONf_plane_restr0.0051184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.3280.38511270.38252462X-RAY DIFFRACTION93.9
3.328-3.47920.39691570.37182564X-RAY DIFFRACTION97.8
3.4792-3.66240.40471590.33452548X-RAY DIFFRACTION98.1
3.6624-3.89130.30691330.29982564X-RAY DIFFRACTION97.8
3.8913-4.1910.35121420.27572561X-RAY DIFFRACTION97.8
4.191-4.61130.32021600.24492583X-RAY DIFFRACTION97.8
4.6113-5.27530.2831540.23022609X-RAY DIFFRACTION97.7
5.2753-6.63380.27631260.24562614X-RAY DIFFRACTION96.6
6.6338-29.47860.19381610.17272672X-RAY DIFFRACTION94.8

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