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- PDB-3oqm: structure of ccpa-hpr-ser46p-ackA2 complex -

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Basic information

Entry
Database: PDB / ID: 3oqm
Titlestructure of ccpa-hpr-ser46p-ackA2 complex
Components
  • 5'-D(*TP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*TP*AP*CP*AP*A)-3'
  • 5'-D(*TP*TP*GP*TP*AP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*A)-3'
  • Catabolite control protein A
  • Phosphocarrier protein HPr
KeywordsTRANSCRIPTION/TRANSFERASE/DNA / PBP fold for ccpa / transcription / HPr-SER46-P and cre DNA / nucleoid / TRANSCRIPTION-TRANSFERASE-DNA complex
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 domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Phosphocarrier protein HPr / Catabolite control protein A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.96 Å
AuthorsSchumacher, M.A. / Sprehe, M. / Bartholomae, M. / Hillen, W. / Brennan, R.G.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse catabolite response element sites reveal the basis for high-affinity binding to degenerate DNA operators.
Authors: Schumacher, M.A. / Sprehe, M. / Bartholomae, M. / Hillen, W. / Brennan, R.G.
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 1.3Nov 20, 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
C: Catabolite control protein A
D: Phosphocarrier protein HPr
E: 5'-D(*TP*TP*GP*TP*AP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*A)-3'
B: 5'-D(*TP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*TP*AP*CP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,92010
Polymers103,5366
Non-polymers3844
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13070 Å2
ΔGint-127 kcal/mol
Surface area37560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.240, 103.540, 176.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACSD

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


Mass: 37724.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: alsA, amyR, BSU29740, ccpA, graR / Production host: Escherichia coli (E. coli) / References: UniProt: P25144
#2: Protein Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9147.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU13900, hpr, ptsH / Production host: Escherichia coli (E. coli)
References: UniProt: P08877, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases

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DNA chain , 2 types, 2 molecules EB

#3: DNA chain 5'-D(*TP*TP*GP*TP*AP*AP*GP*CP*GP*TP*TP*AP*TP*CP*AP*A)-3'


Mass: 4912.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (synth.) Bacillus subtilis (bacteria)
#4: DNA chain 5'-D(*TP*TP*GP*AP*TP*AP*AP*CP*GP*CP*TP*TP*AP*CP*AP*A)-3'


Mass: 4881.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (synth.) Bacillus subtilis (bacteria)

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Non-polymers , 2 types, 54 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, Ammonium sulphate, Mes, magnesium chloride, pH 5.6, 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 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.96→103.7 Å / Num. all: 28989 / Num. obs: 28736 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 250 Å2
Reflection shellResolution: 2.96→3.05 Å / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR
Starting model: 2FEP

2fep


Resolution: 2.96→57.1 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1614441.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2009 6.9 %RANDOM
Rwork0.216 ---
all0.217 28736 --
obs0.216 28726 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5588 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1--10.06 Å20 Å20 Å2
2---1.6 Å20 Å2
3---11.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.96→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6432 650 20 50 7152
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_mcbond_it3.211.5
X-RAY DIFFRACTIONc_mcangle_it5.012
X-RAY DIFFRACTIONc_scbond_it5.292
X-RAY DIFFRACTIONc_scangle_it7.62.5
LS refinement shellResolution: 2.96→3.15 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 347 7.3 %
Rwork0.317 4397 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-NEWSEP.param.txtprotein-NEWSEP.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

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