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- PDB-3kos: Structure of the AmpR effector binding domain from Citrobacter fr... -

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Basic information

Entry
Database: PDB / ID: 3kos
TitleStructure of the AmpR effector binding domain from Citrobacter freundii
ComponentsHTH-type transcriptional activator ampR
KeywordsTRANSCRIPTION / alpha-beta sandwich / Activator / DNA-binding / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional activator AmpR
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsMark, B.L. / Balcewich, M.D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure of the AmpR Effector Binding Domain Provides Insight into the Molecular Regulation of Inducible AmpC beta-Lactamase.
Authors: Balcewich, M.D. / Reeve, T.M. / Orlikow, E.A. / Donald, L.J. / Vocadlo, D.J. / Mark, B.L.
History
DepositionNov 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional activator ampR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,09310
Polymers25,0571
Non-polymers1,0359
Water3,153175
1
A: HTH-type transcriptional activator ampR
hetero molecules

A: HTH-type transcriptional activator ampR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,18520
Polymers50,1152
Non-polymers2,07018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6480 Å2
ΔGint-4 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.280, 34.190, 49.980
Angle α, β, γ (deg.)90.00, 102.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

21A-362-

HOH

31A-364-

HOH

41A-389-

HOH

51A-390-

HOH

61A-395-

HOH

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Components

#1: Protein HTH-type transcriptional activator ampR


Mass: 25057.404 Da / Num. of mol.: 1 / Fragment: UNP residues 83-291, Effector binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: ampR / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) GOLD HTE / References: UniProt: P12529
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 10% PEG 4000, 10% glycerol, 100mM MES pH5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979594, 0.979741, 1.019867
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2006
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9795941
20.9797411
31.0198671
ReflectionResolution: 1.83→28.92 Å / Num. obs: 18564 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.3
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2700 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
PHENIX(phenix.refine: 1.4_129)refinement
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.83→28.071 Å / SU ML: 0.22 / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 1852 10 %random
Rwork0.1703 ---
all0.1735 18517 --
obs0.1735 18517 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.197 Å2 / ksol: 0.4 e/Å3
Refinement stepCycle: LAST / Resolution: 1.83→28.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 66 175 1792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061662
X-RAY DIFFRACTIONf_angle_d1.1552259
X-RAY DIFFRACTIONf_dihedral_angle_d17.758608
X-RAY DIFFRACTIONf_chiral_restr0.07248
X-RAY DIFFRACTIONf_plane_restr0.006281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.89540.21651840.18741655X-RAY DIFFRACTION99
1.8954-1.97130.21131830.17591642X-RAY DIFFRACTION100
1.9713-2.0610.22541800.16841618X-RAY DIFFRACTION100
2.061-2.16960.20691870.16971689X-RAY DIFFRACTION100
2.1696-2.30550.20091820.16291644X-RAY DIFFRACTION100
2.3055-2.48340.23261850.17361651X-RAY DIFFRACTION100
2.4834-2.73310.21841850.1741670X-RAY DIFFRACTION100
2.7331-3.12820.21021860.17271672X-RAY DIFFRACTION100
3.1282-3.93940.17831870.15241681X-RAY DIFFRACTION100
3.9394-28.07380.17341930.17191743X-RAY DIFFRACTION100

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