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- PDB-6kcr: X-ray structure of the MtlR-HPr complex from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 6kcr
TitleX-ray structure of the MtlR-HPr complex from Escherichia coli
Components
  • Mannitol operon repressor
  • Phosphocarrier protein HPr
KeywordsGENE REGULATION / MtlR / HPr / glucose repression of mannitol operon / phosphotransferase system
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity / negative regulation of DNA-templated transcription / cytosol
Similarity search - Function
Mannitol repressor MtlR-like / MtlR-like superfamily / Mannitol repressor / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like ...Mannitol repressor MtlR-like / MtlR-like superfamily / Mannitol repressor / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr / Mannitol operon repressor
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsChoe, M. / Woo, J.S. / Seok, Y.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2018R1A5A1025077 Korea, Republic Of
National Research Foundation (Korea)2019R1A2C2004143 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2019
Title: Structural insight into glucose repression of the mannitol operon.
Authors: Choe, M. / Min, H. / Park, Y.H. / Kim, Y.R. / Woo, J.S. / Seok, Y.J.
History
DepositionJun 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Mannitol operon repressor
B: Phosphocarrier protein HPr
C: Mannitol operon repressor
D: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)63,9394
Polymers63,9394
Non-polymers00
Water00
1
A: Mannitol operon repressor
B: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)31,9692
Polymers31,9692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Mannitol operon repressor
D: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)31,9692
Polymers31,9692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.360, 122.317, 147.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNLEULEU(chain 'A' and resid 26 through 189)AA26 - 18932 - 195
221GLNGLNLEULEUchain 'C'CC26 - 18932 - 195
132METMETGLUGLUchain 'B'BB1 - 851 - 85
242METMETGLUGLUchain 'D'DD1 - 851 - 85

NCS ensembles :
ID
1
2

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Components

#1: Protein Mannitol operon repressor / MtlR / Mannitol repressor protein


Mass: 22839.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: mtlR, b3601, JW3575 / Variant: MG1655 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P0AF10
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9129.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ptsH, hpr, b2415, JW2408 / Variant: MG1655 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P0AA04

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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: 3.43 Å3/Da / Density % sol: 68.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris-HCl (pH 8.5), 200 mM Mg-acetate, 15% polyethylene glycol (PEG) 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 11374 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 121.23 Å2 / Rrim(I) all: 0.079 / Rsym value: 0.072 / Net I/σ(I): 22.3
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 567 / CC1/2: 0.816 / Rrim(I) all: 0.796 / Rsym value: 0.73 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BRJ

3brj


Resolution: 3.5→29.4 Å / SU ML: 0.4309 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.5328
RfactorNum. reflection% reflection
Rfree0.2604 1136 9.99 %
Rwork0.2409 --
obs0.2429 11374 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 139.51 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 0 0 3908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243966
X-RAY DIFFRACTIONf_angle_d0.53135374
X-RAY DIFFRACTIONf_chiral_restr0.0379637
X-RAY DIFFRACTIONf_plane_restr0.0029699
X-RAY DIFFRACTIONf_dihedral_angle_d8.29052428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.660.34721380.32021238X-RAY DIFFRACTION98.71
3.66-3.850.33781420.30491278X-RAY DIFFRACTION99.86
3.85-4.090.31281390.28381261X-RAY DIFFRACTION99.72
4.09-4.410.27131400.25841259X-RAY DIFFRACTION99.79
4.41-4.850.27071420.24221281X-RAY DIFFRACTION99.72
4.85-5.540.29361420.25581273X-RAY DIFFRACTION99.79
5.54-6.970.30961450.2911309X-RAY DIFFRACTION99.79
6.97-29.40.19161480.18191339X-RAY DIFFRACTION98.15

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