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- PDB-1rxx: Structure of arginine deiminase -

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Basic information

Entry
Database: PDB / ID: 1rxx
TitleStructure of arginine deiminase
ComponentsArginine deiminase
KeywordsHYDROLASE / arginine degradation pathway / L-arginine deiminase / catalytic mechanism / Structure 2 Function Project / S2F / Structural Genomics
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 / SYNCHROTRON / MAD / Resolution: 2.45 Å
AuthorsGalkin, A. / Kulakova, L. / Sarikaya, E. / Lim, K. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural insight into arginine degradation by arginine deiminase, an antibacterial and parasite drug target.
Authors: Galkin, A. / Kulakova, L. / Sarikaya, E. / Lim, K. / Howard, A. / Herzberg, O.
History
DepositionDec 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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)189,1564
Polymers189,1564
Non-polymers00
Water8,863492
1
A: Arginine deiminase
B: Arginine deiminase

A: Arginine deiminase
B: Arginine deiminase


Theoretical massNumber of molelcules
Total (without water)189,1564
Polymers189,1564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
MethodPQS
2
C: Arginine deiminase
D: Arginine deiminase

C: Arginine deiminase
D: Arginine deiminase


Theoretical massNumber of molelcules
Total (without water)189,1564
Polymers189,1564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
MethodPQS
3
D: Arginine deiminase

D: Arginine deiminase


Theoretical massNumber of molelcules
Total (without water)94,5782
Polymers94,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3370 Å2
ΔGint-22 kcal/mol
Surface area31060 Å2
MethodPISA
4
A: Arginine deiminase

B: Arginine deiminase


Theoretical massNumber of molelcules
Total (without water)94,5782
Polymers94,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3330 Å2
ΔGint-23 kcal/mol
Surface area32060 Å2
MethodPISA
5
C: Arginine deiminase

C: Arginine deiminase


Theoretical massNumber of molelcules
Total (without water)94,5782
Polymers94,5782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3500 Å2
ΔGint-18 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.900, 114.900, 300.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a tetramer generated from the molecules A and B in the asymmetric unit by the operations: Y, X, -Z / The biological assembly is a tetramer generated from the molecules C and D in the asymmetric unit by the operations: -Y, -X, -Z+1/2

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Components

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


Mass: 47289.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ARCA, PA5171 / Plasmid: PET100-ADIH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P13981, arginine deiminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 53.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 33% MPD (2-methyl-2,4-pentanediol), 6% PEG 3350, 0.1 M Tris-HCl (pH 7.6), and 4% acetone, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1droppH7.5
20.1 M1dropNaCl
333 %MPD1reservoir
46 %PEG33501reservoir
50.1 MTris-HCl1reservoirpH7.6
64 %acetone1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.98400, 0.96788, 0.97925, 0.97939
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2003
RadiationMonochromator: Si(111) double crystal system / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9841
20.967881
30.979251
40.979391
ReflectionResolution: 2.45→20 Å / Num. obs: 74771 / % possible obs: 99.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 14
Reflection shellResolution: 2.45→2.55 Å / Rmerge(I) obs: 0.416 / % possible all: 100
Reflection
*PLUS
Num. measured all: 829494
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3802 -random
Rwork0.198 ---
all-74771 --
obs-74675 99.9 %-
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12695 0 0 492 13187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 2.45→2.47 Å
RfactorNum. reflection
Rfree0.344 73
Rwork0.281 -
obs-1380
Refinement
*PLUS
Num. reflection obs: 73248
Solvent computation
*PLUS
Displacement parameters
*PLUS

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