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- PDB-1lxy: Crystal Structure of Arginine Deiminase covalently linked with L-... -

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Basic information

Entry
Database: PDB / ID: 1lxy
TitleCrystal Structure of Arginine Deiminase covalently linked with L-citrulline
ComponentsArginine Deiminase
KeywordsHYDROLASE / deiminase / 5-fold pseudo-symmetric domain / 5-Helix bundle domain
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
CITRULLINE / Arginine deiminase
Similarity search - Component
Biological speciesMycoplasma arginini (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsDas, K. / Buttler, G.H. / Kwiatkowski, V. / Yadav, P. / Arnold, E.
CitationJournal: Structure / Year: 2004
Title: Crystal structures of arginine deiminase with covalent reaction intermediates; implications for catalytic mechanism
Authors: Das, K. / Buttler, G.H. / Kwiatkowski, V. / Clark Jr., A.D. / Yadav, P. / Arnold, E.
History
DepositionJun 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Arginine Deiminase
B: Arginine Deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,4596
Polymers92,8642
Non-polymers5954
Water9,908550
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.240, 76.370, 82.900
Angle α, β, γ (deg.)90.00, 109.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Arginine Deiminase / E.C.3.5.3.6 / ADI / Arginine dihydrolase / AD


Mass: 46431.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: 5-fold pseudosymmetric guanidino group modifying enzyme
Source: (natural) Mycoplasma arginini (bacteria) / References: UniProt: P23793, arginine deiminase
#2: Chemical ChemComp-CIR / CITRULLINE


Type: L-peptide linking / Mass: 175.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13N3O3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.31 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 6000, Potassium phosphate, L-citrulline, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 282K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
20.01 Mpotassium phosphate1droppH7.0
318 %PEG60001reservoir
40.1 Mpotassium phosphate1reservoirpH6.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21051
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJun 15, 1997
RIGAKU RAXIS II2IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.54181
ReflectionResolution: 2→99 Å / Num. all: 59662 / Num. obs: 59662 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.083 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4.6 / % possible all: 90.4
Reflection
*PLUS
Highest resolution: 2 Å / Redundancy: 3.37 %
Reflection shell
*PLUS
% possible obs: 90.4 % / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2→19.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1799833.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2933 5.1 %RANDOM
Rwork0.186 ---
obs0.1861 58076 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.548 Å2 / ksol: 0.361371 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å20 Å22.03 Å2
2---2.28 Å20 Å2
3----2.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 40 550 7130
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it3.331.5
X-RAY DIFFRACTIONc_mcangle_it3.732
X-RAY DIFFRACTIONc_scbond_it4.222
X-RAY DIFFRACTIONc_scangle_it4.852.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 457 5 %
Rwork0.24 8613 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TRS.PARTRS.TOP
X-RAY DIFFRACTION4SUB.PARSUB.TOP
X-RAY DIFFRACTION5PARAMETER_INFILE_5TOPOLOGY_INFILE_5
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Rfactor all: 4.8
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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