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- PDB-2fep: Structure of truncated CcpA in complex with P-Ser-HPr and Sulfate ions -

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Basic information

Entry
Database: PDB / ID: 2fep
TitleStructure of truncated CcpA in complex with P-Ser-HPr and Sulfate ions
Components
  • Catabolite control protein A
  • Phosphocarrier protein HPr
KeywordsTRANSCRIPTION / CcpA / HPr / transcriptional regulator
Function / homology
Function and homology information


regulation of carbohydrate utilization / phosphoenolpyruvate-dependent sugar phosphotransferase system / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / 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 / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. ...Catabolite control protein A / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / PTS HPR domain serine phosphorylation site signature. / 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 subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChaptal, V. / Gueguen-Chaignon, V. / Poncet, S. / Lecampion, C. / Meyer, P. / Deutscher, J. / Galinier, A. / Nessler, S.
CitationJournal: Proteins / Year: 2006
Title: Structural analysis of B. subtilis CcpA effector binding site.
Authors: Chaptal, V. / Gueguen-Chaignon, V. / Poncet, S. / Lecampion, C. / Meyer, P. / Deutscher, J. / Galinier, A. / Nessler, S. / Morera, S.
History
DepositionDec 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catabolite control protein A
S: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7505
Polymers41,4622
Non-polymers2883
Water1,910106
1
A: Catabolite control protein A
S: Phosphocarrier protein HPr
hetero molecules

A: Catabolite control protein A
S: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,50010
Polymers82,9244
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)67.620, 67.620, 167.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a dimer generated from the monomer in the asymetric unit by a two fold crystallographic axis

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Components

#1: Protein Catabolite control protein A / Glucose-resistance amylase regulator


Mass: 32183.639 Da / Num. of mol.: 1 / Fragment: residues 61-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ccpA, alsA, amyR, graR / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P25144
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9278.313 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ptsH / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P08877
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate 3.5M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2004
RadiationMonochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 14948 / Num. obs: 14933 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 34 Å2 / Rsym value: 0.091 / Net I/σ(I): 6
Reflection shellResolution: 2.45→2.58 Å / Mean I/σ(I) obs: 2 / Num. unique all: 2132 / Rsym value: 0.36 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1RZR

1rzr


Resolution: 2.45→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 1041 random
Rwork0.209 --
all-14948 -
obs-14933 -
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 15 106 2885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_d1.22

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