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- PDB-2aci: Structure of D166A arginine deiminase -

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Basic information

Entry
Database: PDB / ID: 2aci
TitleStructure of D166A arginine deiminase
ComponentsArginine deiminase
KeywordsHYDROLASE / arginine degradation pathway / L-arginine deiminase / catalytic mechanism
Function / homology
Function and homology information


arginine deiminase / arginine deiminase activity / arginine deiminase pathway / arginine catabolic process to ornithine / cytoplasm
Similarity search - Function
Pentein / Arginine deiminase / Arginine deiminase / Arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsGalkin, A. / Lu, X. / Dunaway-Mariano, D. / Herzberg, O.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structures Representing the Michaelis Complex and the Thiouronium Reaction Intermediate of Pseudomonas aeruginosa Arginine Deiminase.
Authors: Galkin, A. / Lu, X. / Dunaway-Mariano, D. / Herzberg, O.
History
DepositionJul 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginine deiminase
B: Arginine deiminase
C: Arginine deiminase
D: Arginine deiminase


Theoretical massNumber of molelcules
Total (without water)185,7884
Polymers185,7884
Non-polymers00
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Arginine deiminase
D: Arginine deiminase


Theoretical massNumber of molelcules
Total (without water)92,8942
Polymers92,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-24 kcal/mol
Surface area31770 Å2
MethodPISA
3
B: Arginine deiminase
C: Arginine deiminase


Theoretical massNumber of molelcules
Total (without water)92,8942
Polymers92,8942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-23 kcal/mol
Surface area31730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.2, 123.9, 150.0
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer generated from the molecules A, B, C and D in the asymmetric unit

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Components

#1: Protein
Arginine deiminase / ADI / Arginine dihydrolase / AD


Mass: 46446.875 Da / Num. of mol.: 4 / Mutation: D166A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: arcA / Plasmid: PET100-ADIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P13981, arginine deiminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 36% MPD (2-methyl-2,4-pentanediol), 6% PEG 3350, 0.1 M Tris-HCl (pH 7.6), L-arginine 0.02 M , VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 22, 2004
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 59388 / Num. obs: 55706 / % possible obs: 93.8 % / Rmerge(I) obs: 0.097
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.361 / % possible all: 92.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalClear(MSC/RIGAKU)data reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2A9G

2a9g


Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 2815 random
Rwork0.198 --
all-55706 -
obs-55661 -
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12653 0 0 300 12953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection
Rfree0.387 270
Rwork0.323 -
obs-5427

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