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- PDB-1sxg: Structural studies on the apo transcription factor form B. megaterium -

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Basic information

Entry
Database: PDB / ID: 1sxg
TitleStructural studies on the apo transcription factor form B. megaterium
ComponentsGlucose-resistance amylase regulator
KeywordsTRANSCRIPTION / allosterism / phosphoprotein / transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Catabolite control protein A / 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 domain superfamily / Response regulator ...Catabolite control protein A / 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 domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-PHENYLAMINO-ETHANESULFONIC ACID / Catabolite control protein A
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
B: Glucose-resistance amylase regulator
I: Glucose-resistance amylase regulator
P: Glucose-resistance amylase regulator
F: Glucose-resistance amylase regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,3558
Polymers185,9536
Non-polymers4022
Water2,504139
1
A: Glucose-resistance amylase regulator
D: Glucose-resistance amylase regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1853
Polymers61,9842
Non-polymers2011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-4 kcal/mol
Surface area20880 Å2
MethodPISA
2
B: Glucose-resistance amylase regulator
I: Glucose-resistance amylase regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1853
Polymers61,9842
Non-polymers2011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
P: Glucose-resistance amylase regulator
F: Glucose-resistance amylase regulator


Theoretical massNumber of molelcules
Total (without water)61,9842
Polymers61,9842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)375.390, 60.140, 75.650
Angle α, β, γ (deg.)90.00, 95.59, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 30992.119 Da / Num. of mol.: 6 / Mutation: residues 53-332
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-171 / 2-PHENYLAMINO-ETHANESULFONIC ACID


Mass: 201.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.35 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 3350, CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.71→75.29 Å / Num. all: 44614 / Num. obs: 44614 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 57 Å2 / Rsym value: 0.084
Reflection shellResolution: 2.75→2.92 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P212121 apo structure

Resolution: 2.75→75.29 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2087670.52 / 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
Rfree0.263 4413 10.1 %RANDOM
Rwork0.214 ---
all0.223 43833 --
obs0.2141 43817 98.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0764 Å2 / ksol: 0.335193 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.74 Å20 Å20.38 Å2
2---2.81 Å20 Å2
3---6.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.75→75.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12774 0 26 139 12939
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 681 9.8 %
Rwork0.334 6238 -
obs--94.6 %
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 OTHER REFINEMENT REMARKS: NULL

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