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- PDB-1rzr: crystal structure of transcriptional regulator-phosphoprotein-DNA... -

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Basic information

Entry
Database: PDB / ID: 1rzr
Titlecrystal structure of transcriptional regulator-phosphoprotein-DNA complex
Components
  • (Glucose-resistance amylase ...) x 2
  • 5'-D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3'
  • 5'-D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3'
  • Phosphocarrier protein HPr
Keywordstranscription/transport protein/DNA / protein-DNA complex / phospho-protein / transcription-transport protein-DNA COMPLEX
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / transcription cis-regulatory region binding / DNA-binding transcription factor activity / 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 ...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. / Transcriptional regulator LacI/GalR-like, sensor domain / LacI-type HTH domain signature. / 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 megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSchumacher, M.A. / Allen, G.S. / Brennan, R.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P.
Authors: Schumacher, M.A. / Allen, G.S. / Diel, M. / Seidel, G. / Hillen, W. / Brennan, R.G.
History
DepositionDec 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 5'-D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3'
R: 5'-D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3'
E: 5'-D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3'
B: 5'-D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3'
G: Glucose-resistance amylase regulator
C: Glucose-resistance amylase regulator
A: Glucose-resistance amylase regulator
D: Glucose-resistance amylase regulator
T: Phosphocarrier protein HPr
L: Phosphocarrier protein HPr
Y: Phosphocarrier protein HPr
S: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,71421
Polymers204,99312
Non-polymers7219
Water1,56787
1
H: 5'-D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3'
R: 5'-D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3'
G: Glucose-resistance amylase regulator
C: Glucose-resistance amylase regulator
T: Phosphocarrier protein HPr
L: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,00011
Polymers102,5206
Non-polymers4805
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-D(*CP*TP*GP*AP*AP*AP*GP*CP*GP*CP*TP*AP*AP*CP*AP*G)-3'
B: 5'-D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3'
A: Glucose-resistance amylase regulator
D: Glucose-resistance amylase regulator
Y: Phosphocarrier protein HPr
S: Phosphocarrier protein HPr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,71410
Polymers102,4736
Non-polymers2414
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.710, 109.240, 117.810
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules HERB

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


Mass: 4916.220 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*GP*TP*TP*AP*GP*CP*GP*CP*TP*TP*TP*CP*AP*G)-3'


Mass: 4880.164 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Glucose-resistance amylase ... , 2 types, 4 molecules GCAD

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


Mass: 37154.598 Da / Num. of mol.: 3 / Fragment: transcriptional regulator
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CCPA / Production host: Escherichia coli (E. coli) / References: UniProt: P46828
#4: Protein Glucose-resistance amylase regulator / Catabolite control protein


Mass: 37107.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CCPA / Production host: Escherichia coli (E. coli) / References: UniProt: P46828

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Protein , 1 types, 4 molecules TLYS

#5: Protein
Phosphocarrier protein HPr / Histidine-containing protein


Mass: 9207.212 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: PTSH / Production host: Escherichia coli (E. coli) / References: UniProt: O69250

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Non-polymers , 3 types, 96 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 3.44 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulphate11
2H2O11
3ammonium sulphate12
4H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 / Wavelength: 0.9794, 0.9184, 0.9796
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2003
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97941
30.91841
40.97961
ReflectionResolution: 2.8→78.7 Å / Num. all: 57469 / Num. obs: 57469 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 61.5 Å2
Reflection shellResolution: 2.8→2.89 Å / % possible all: 78

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→78.7 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1722050 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 5845 10.2 %RANDOM
Rwork0.242 ---
obs0.242 54639 86.8 %-
all-57480 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 92.4635 Å2 / ksol: 0.367497 e/Å3
Displacement parametersBiso mean: 80.2 Å2
Baniso -1Baniso -2Baniso -3
1--29.45 Å20 Å20 Å2
2--49.03 Å20 Å2
3----19.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.8→78.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12770 1300 37 87 14194
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.47
X-RAY DIFFRACTIONc_mcbond_it3.41.5
X-RAY DIFFRACTIONc_mcangle_it5.42
X-RAY DIFFRACTIONc_scbond_it7.792
X-RAY DIFFRACTIONc_scangle_it9.542.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.44 635 10.5 %
Rwork0.398 5401 -
obs--55 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP-NPROTEIN-NEWSE
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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