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- PDB-1sxh: apo structure of B. megaterium transcription regulator -

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Basic information

Entry
Database: PDB / ID: 1sxh
Titleapo structure of B. megaterium transcription regulator
ComponentsGlucose-resistance amylase regulator
KeywordsTRANSCRIPTION / allosterism / phosphoprotein / transcription regulation / GRam positive bacteria / CCR
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Catabolite control protein A / 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 ...Catabolite control protein A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Catabolite control protein A
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.75 Å
AuthorsSchumacher, M.A. / Allen, G.S. / Diel, M. / Seidel, G. / Hillen, W. / Brennan, R.G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural studies on the apo transcription factor form B. megaterium
Authors: Schumacher, M.A. / Allen, G.S. / Diel, M. / Seidel, G. / Hillen, W. / Brennan, R.G.
History
DepositionMar 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Glucose-resistance amylase regulator
D: Glucose-resistance amylase regulator


Theoretical massNumber of molelcules
Total (without water)62,7352
Polymers62,7352
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.680, 72.190, 105.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 31367.271 Da / Num. of mol.: 2 / Mutation: residues 53-332
Source method: isolated from a genetically manipulated source
Details: apo form / Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: CCpa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P46828
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.31 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, 0.2 M NaCl, HEPES, 7.5, 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: 1.08
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.75→59.91 Å / Num. all: 15082 / Num. obs: 15039 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 48.8 Å2
Reflection shellResolution: 2.75→2.92 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR
Starting model: protein-DNA bound form, C-subdomains only

Resolution: 2.75→59.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1150093.15 / 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
Rfree0.273 2321 15.4 %RANDOM
Rwork0.241 ---
all0.242 7531 --
obs0.241 7531 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.4387 Å2 / ksol: 0.266395 e/Å3
Displacement parametersBiso mean: 62.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--8.46 Å20 Å2
3----9.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.75→59.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4246 0 0 41 4287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.04
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 349 14.1 %
Rwork0.383 2124 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CHES_XPLOR_PAR.TXTCHES_XPLOR_TOP.TXT
X-RAY DIFFRACTION4ION.PARAMION.TOP

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