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- PDB-3bp8: Crystal structure of Mlc/EIIB complex -

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Basic information

Entry
Database: PDB / ID: 3bp8
TitleCrystal structure of Mlc/EIIB complex
Components
  • PTS system glucose-specific EIICB component
  • Putative NAGC-like transcriptional regulator
KeywordsTRANSCRIPTION / enzyme / IICBGlc / glucose signaling / Mlc / protein-protein interaction / transcription regulation / Inner membrane / Kinase / Membrane / Phosphoprotein / Phosphotransferase system / Sugar transport / Transferase / Transmembrane / Transport
Function / homology
Function and homology information


protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / : / D-glucose import across plasma membrane / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / DNA-templated transcription ...protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / : / D-glucose import across plasma membrane / D-glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Glucose permease domain IIB / Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific 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. ...Glucose permease domain IIB / Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific 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 / ROK family / ROK family / Gyrase A; domain 2 / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DNA-binding transcriptional repressor Mlc / PTS system glucose-specific EIICB component / Transcriptional repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsAn, Y.J. / Jung, H.I. / Cha, S.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Analyses of Mlc-IIBGlc interaction and a plausible molecular mechanism of Mlc inactivation by membrane sequestration
Authors: Nam, T.W. / Jung, H.I. / An, Y.J. / Park, Y.H. / Lee, S.H. / Seok, Y.J. / Cha, S.S.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative NAGC-like transcriptional regulator
B: Putative NAGC-like transcriptional regulator
C: PTS system glucose-specific EIICB component
D: PTS system glucose-specific EIICB component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5109
Polymers104,2024
Non-polymers3085
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative NAGC-like transcriptional regulator
B: Putative NAGC-like transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9887
Polymers88,6802
Non-polymers3085
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-25.6 kcal/mol
Surface area33450 Å2
MethodPISA
3
C: PTS system glucose-specific EIICB component


Theoretical massNumber of molelcules
Total (without water)7,7611
Polymers7,7611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PTS system glucose-specific EIICB component


Theoretical massNumber of molelcules
Total (without water)7,7611
Polymers7,7611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)201.427, 55.424, 82.460
Angle α, β, γ (deg.)90.00, 95.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative NAGC-like transcriptional regulator / Mlc


Mass: 44339.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B834(DE3) / Gene: mlc / Plasmid: pNS100 / Production host: Escherichia Coli (E. coli) / References: UniProt: Q8X787, UniProt: P50456*PLUS
#2: Protein PTS system glucose-specific EIICB component / EIIB / EIICB-Glc / EII-Glc


Mass: 7760.941 Da / Num. of mol.: 2 / Fragment: UNP residues 401-475
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GI698 / Gene: ptsG, glcA, umg / Plasmid: pJHK / Production host: Escherichia Coli (E. coli) / References: UniProt: P69786
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growpH: 5.5 / Details: 6% PEG 6K, 0.1M MgCl2, 0.1M sodium acetate, pH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B
DetectorDate: Dec 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.85→20 Å / Num. obs: 20356 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.6 Å2

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Processing

Software
NameVersionClassification
PROTEUM PLUS300data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z6R, 3BP3

1z6r

3bp3


Resolution: 2.85→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 206924.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1748 9.8 %RANDOM
Rwork0.228 ---
obs0.228 17850 83.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.192161 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1-17.58 Å20 Å211.57 Å2
2--4.01 Å20 Å2
3---13.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å0.82 Å
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6929 0 14 0 6943
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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