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- PDB-3u33: Crystal Structure of the E. coli adaptive response protein AidB i... -

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Basic information

Entry
Database: PDB / ID: 3u33
TitleCrystal Structure of the E. coli adaptive response protein AidB in the space group P3(2)
ComponentsPutative acyl-CoA dehydrogenase AidB
KeywordsOXIDOREDUCTASE / acyl-coenzyme A dehydrogenase / protective function in the presence of alkylating agents / DNA binding / FAD binding
Function / homology
Function and homology information


isovaleryl-CoA dehydrogenase activity / Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / 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 K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWong, C. / Jost, M. / Drennan, C.L.
CitationJournal: Biochemistry / Year: 2011
Title: Flavin-induced oligomerization in Escherichia coli adaptive response protein AidB.
Authors: Hamill, M.J. / Jost, M. / Wong, C. / Elliott, S.J. / Drennan, C.L.
History
DepositionOct 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Sep 13, 2023Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acyl-CoA dehydrogenase AidB
B: Putative acyl-CoA dehydrogenase AidB
C: Putative acyl-CoA dehydrogenase AidB
D: Putative acyl-CoA dehydrogenase AidB
E: Putative acyl-CoA dehydrogenase AidB
F: Putative acyl-CoA dehydrogenase AidB
G: Putative acyl-CoA dehydrogenase AidB
H: Putative acyl-CoA dehydrogenase AidB
I: Putative acyl-CoA dehydrogenase AidB
J: Putative acyl-CoA dehydrogenase AidB
K: Putative acyl-CoA dehydrogenase AidB
L: Putative acyl-CoA dehydrogenase AidB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)737,80636
Polymers727,95412
Non-polymers9,85224
Water5,350297
1
A: Putative acyl-CoA dehydrogenase AidB
B: Putative acyl-CoA dehydrogenase AidB
C: Putative acyl-CoA dehydrogenase AidB
D: Putative acyl-CoA dehydrogenase AidB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,93512
Polymers242,6514
Non-polymers3,2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26740 Å2
ΔGint-152 kcal/mol
Surface area67980 Å2
MethodPISA
2
E: Putative acyl-CoA dehydrogenase AidB
F: Putative acyl-CoA dehydrogenase AidB
G: Putative acyl-CoA dehydrogenase AidB
H: Putative acyl-CoA dehydrogenase AidB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,93512
Polymers242,6514
Non-polymers3,2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26880 Å2
ΔGint-154 kcal/mol
Surface area67900 Å2
MethodPISA
3
I: Putative acyl-CoA dehydrogenase AidB
J: Putative acyl-CoA dehydrogenase AidB
K: Putative acyl-CoA dehydrogenase AidB
L: Putative acyl-CoA dehydrogenase AidB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,93512
Polymers242,6514
Non-polymers3,2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26740 Å2
ΔGint-157 kcal/mol
Surface area67960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.720, 179.720, 204.237
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A or chain B) and (resseq 2:162 or resseq...
211(chain D or chain C) and (resseq 2:162 or resseq...
311(chain E or chain F) and (resseq 2:162 or resseq...
411(chain H or chain G) and (resseq 2:162 or resseq...
511(chain I or chain J) and (resseq 2:162 or resseq...
611(chain L or chain K) and (resseq 2:162 or resseq...
DetailsThree tetramers in the asymmetric unit, composed of A+B+C+D, E+F+G+H, and I+J+K+L. Tetrameric assembly independently confirmed by analytical ultracentrifugation.

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Components

#1: Protein
Putative acyl-CoA dehydrogenase AidB / adaptive response protein AidB


Mass: 60662.824 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: AB1157 / Gene: aidB, b4187, JW5867 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P33224, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (v/v) ethanol, 0.1 M HEPES pH 7.5, 0.2 M magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2008
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 174735 / Num. obs: 174735 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 45.1 Å2 / Rsym value: 0.095 / Net I/σ(I): 14.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.33 / Num. unique all: 17687 / Rsym value: 0.457 / % possible all: 97.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DJL

3djl


Resolution: 2.8→46.254 Å / SU ML: 0.78 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 8633 5.01 %random
Rwork0.2045 ---
obs0.2058 172442 94.99 %-
all-174695 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.302 Å2 / ksol: 0.278 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2626 Å2-0 Å2-0 Å2
2--1.2626 Å2-0 Å2
3----0.8276 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49649 0 648 297 50594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00551457
X-RAY DIFFRACTIONf_angle_d0.82869861
X-RAY DIFFRACTIONf_dihedral_angle_d12.75218559
X-RAY DIFFRACTIONf_chiral_restr0.0547635
X-RAY DIFFRACTIONf_plane_restr0.0039037
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A7875X-RAY DIFFRACTIONPOSITIONAL
12D7875X-RAY DIFFRACTIONPOSITIONAL0.051
13E7884X-RAY DIFFRACTIONPOSITIONAL0.044
14H7888X-RAY DIFFRACTIONPOSITIONAL0.047
15I7904X-RAY DIFFRACTIONPOSITIONAL0.047
16L7849X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.83220.35172720.30915385X-RAY DIFFRACTION94
2.8322-2.86550.32873000.29655456X-RAY DIFFRACTION95
2.8655-2.90050.32773220.29365443X-RAY DIFFRACTION95
2.9005-2.93720.32012890.28645440X-RAY DIFFRACTION96
2.9372-2.97580.29642860.27475553X-RAY DIFFRACTION96
2.9758-3.01660.28342860.25875550X-RAY DIFFRACTION97
3.0166-3.05970.31052710.26055674X-RAY DIFFRACTION97
3.0597-3.10530.282920.25065586X-RAY DIFFRACTION98
3.1053-3.15380.26993130.24175654X-RAY DIFFRACTION98
3.1538-3.20550.2742980.23745638X-RAY DIFFRACTION98
3.2055-3.26080.24552680.2235620X-RAY DIFFRACTION98
3.2608-3.32010.23663080.21925677X-RAY DIFFRACTION99
3.3201-3.38390.25093120.20865646X-RAY DIFFRACTION99
3.3839-3.4530.24043060.22255681X-RAY DIFFRACTION98
3.453-3.5280.22742810.20665632X-RAY DIFFRACTION98
3.528-3.61010.22132830.21145672X-RAY DIFFRACTION98
3.6101-3.70030.5042680.49711564X-RAY DIFFRACTION35
3.7003-3.80030.2232530.20044970X-RAY DIFFRACTION88
3.8003-3.91210.23872740.20325378X-RAY DIFFRACTION94
3.9121-4.03830.21112880.16535323X-RAY DIFFRACTION93
4.0383-4.18250.1683310.15265786X-RAY DIFFRACTION100
4.1825-4.34990.16452970.14695700X-RAY DIFFRACTION100
4.3499-4.54770.19532990.14615729X-RAY DIFFRACTION100
4.5477-4.78720.18172950.15435739X-RAY DIFFRACTION100
4.7872-5.08680.19923170.16845713X-RAY DIFFRACTION100
5.0868-5.4790.19372980.18455732X-RAY DIFFRACTION100
5.479-6.02930.21693230.19015750X-RAY DIFFRACTION100
6.0293-6.89920.23443070.19885763X-RAY DIFFRACTION100
6.8992-8.68290.1742910.15895705X-RAY DIFFRACTION100
8.6829-46.260.19453050.18195650X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3718-0.1588-0.01770.4984-0.00470.56610.0222-0.1122-0.21250.18480.05430.13420.15610.12010.0165-0.2294-0.0797-0.03350.02970.08520.0371-5.78314.329-67.0106
20.67710.0384-0.05920.4085-0.08180.5906-0.06740.0564-0.10120.11090.0980.0592-0.0029-0.09090.00190.02980.08470.01780.1211-0.08670.037479.994438.9685-74.3771
30.3805-0.08610.23460.5358-0.12260.86450.47960.16490.2903-0.0106-0.04560.0151-0.0371-0.10690.0885-0.4707-0.35620.3063-0.44080.2166-0.239615.0837101.4308-72.1579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain A or chain B or chain C or chain D)
2X-RAY DIFFRACTION2((chain E or chain F or chain G or chain H)
3X-RAY DIFFRACTION3((chain I or chain J or chain K or chain L)

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