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- PDB-2oen: Structural mechanism for the fine-tuning of CcpA function by the ... -

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Basic information

Entry
Database: PDB / ID: 2oen
TitleStructural mechanism for the fine-tuning of CcpA function by the small molecule effectors glucose-6-phosphate and fructose-1,6-bisphosphate
Components
  • Catabolite control protein
  • Phosphocarrier protein HPr
KeywordsTRANSCRIPTION / ccpa / ccr / hpr / crh / protein-dna / adjunct corepressor
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Catabolite control protein A / 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 ...Catabolite control protein A / 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. / LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr / Catabolite control protein A
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.17 Å
AuthorsSchumacher, M.A. / Seidel, G. / Hillen, W. / Brennan, R.G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Mechanism for the Fine-tuning of CcpA Function by The Small Molecule Effectors Glucose 6-Phosphate and Fructose 1,6-Bisphosphate.
Authors: Schumacher, M.A. / Seidel, G. / Hillen, W. / Brennan, R.G.
History
DepositionDec 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Catabolite control protein
L: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)40,1992
Polymers40,1992
Non-polymers00
Water0
1
G: Catabolite control protein
L: Phosphocarrier protein HPr

G: Catabolite control protein
L: Phosphocarrier protein HPr


Theoretical massNumber of molelcules
Total (without water)80,3994
Polymers80,3994
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)69.330, 69.330, 229.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Catabolite control protein


Mass: 30992.119 Da / Num. of mol.: 1 / Fragment: delta CCpa (residues 53-332)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: ccpA / Plasmid: pet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(DE3) / References: UniProt: P46828
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9207.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: ptsH / Plasmid: pet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(DE3) / References: UniProt: O69250

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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: 64.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: ammonium sulphate, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.03
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 23, 2005 / Details: graphite
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3.17→66.4 Å / Num. all: 10182 / Num. obs: 10070 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 89 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.06 / Net I/σ(I): 12
Reflection shellResolution: 3.17→3.37 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1452 / Rsym value: 0.34 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NZU

2nzu


Resolution: 3.17→66.37 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 2692429.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1018 10.1 %RANDOM
Rwork0.278 ---
all0.279 10182 --
obs0.278 10070 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2302 Å2 / ksol: 0.367931 e/Å3
Displacement parametersBiso mean: 74.8 Å2
Baniso -1Baniso -2Baniso -3
1-17.64 Å20 Å20 Å2
2--17.64 Å20 Å2
3----35.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.77 Å0.64 Å
Luzzati d res low-5 Å
Luzzati sigma a1.06 Å1.07 Å
Refinement stepCycle: LAST / Resolution: 3.17→66.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2773 0 0 0 2773
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 3.17→3.37 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.39 171 10.5 %
Rwork0.32 1452 -
obs-1452 99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-NEWSEP.paramprotein-NEWSEP.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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