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- PDB-3djl: Crystal structure of alkylation response protein E. coli AidB -

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Basic information

Entry
Database: PDB / ID: 3djl
TitleCrystal structure of alkylation response protein E. coli AidB
ComponentsProtein aidB
KeywordsOXIDOREDUCTASE / alpha helix / beta-barrel / FAD / Flavoprotein
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / 3-methylbutanoyl-CoA dehydrogenase activity / acyl-CoA dehydrogenase activity / sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 2 - #20 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #600 / Putative acyl-CoA dehydrogenase AidB / Adaptive response protein AidB, N-terminal / Adaptive response protein AidB N-terminal domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal ...Butyryl-CoA Dehydrogenase, subunit A; domain 2 - #20 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #600 / Putative acyl-CoA dehydrogenase AidB / Adaptive response protein AidB, N-terminal / Adaptive response protein AidB N-terminal domain / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Putative acyl-CoA dehydrogenase AidB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsEichman, B.F. / Metz, A.H. / Bowles, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structure and DNA binding of alkylation response protein AidB.
Authors: Bowles, T. / Metz, A.H. / O'Quin, J. / Wawrzak, Z. / Eichman, B.F.
History
DepositionJun 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references / Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein aidB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4883
Polymers60,6631
Non-polymers8262
Water7,909439
1
A: Protein aidB
hetero molecules

A: Protein aidB
hetero molecules

A: Protein aidB
hetero molecules

A: Protein aidB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,95412
Polymers242,6514
Non-polymers3,3038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-x-2,-y,z1
crystal symmetry operation3_355-x-2,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area25500 Å2
ΔGint-155 kcal/mol
Surface area68120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.989, 101.875, 137.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Protein aidB


Mass: 60662.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: aidB / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: P33224
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris pH 8.0, 50 mM CaCl2, and 4% PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.02891 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02891 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 62854 / Num. obs: 62854 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.053 / Net I/σ(I): 80.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6 % / Mean I/σ(I) obs: 8.8 / Num. unique all: 4844 / Rsym value: 0.223 / % possible all: 74.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→41.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.996 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.095 / ESU R Free: 0.088
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: TLS refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.17876 3170 5 %RANDOM
Rwork0.16089 ---
all0.1618 59648 --
obs0.1618 59648 95.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.887 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.67 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4127 0 54 439 4620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0214324
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9715867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78323.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6561534
X-RAY DIFFRACTIONr_chiral_restr0.1130.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213271
X-RAY DIFFRACTIONr_mcbond_it0.9561.52671
X-RAY DIFFRACTIONr_mcangle_it1.71724254
X-RAY DIFFRACTIONr_scbond_it2.98131653
X-RAY DIFFRACTIONr_scangle_it4.5114.51613
LS refinement shellResolution: 1.7→1.792 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.23 363 -
Rwork0.182 6889 -
obs-6889 76.61 %
Refinement TLS params.Method: refined / Origin x: -76.1002 Å / Origin y: -14.7456 Å / Origin z: -24.6689 Å
111213212223313233
T-0.0132 Å2-0.0064 Å20.0094 Å2--0.0233 Å2-0.0166 Å2---0.0169 Å2
L0.2836 °20.0115 °20.0626 °2-0.1745 °20.0286 °2--0.2147 °2
S-0.0126 Å °0.0398 Å °-0.0519 Å °-0.0249 Å °0.0161 Å °-0.008 Å °0.0306 Å °0.0262 Å °-0.0034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 5403 - 540
2X-RAY DIFFRACTION1AC542 - 6021

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