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- PDB-4e4j: Crystal structure of arginine deiminase from Mycoplasma penetrans -

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Basic information

Entry
Database: PDB / ID: 4e4j
TitleCrystal structure of arginine deiminase from Mycoplasma penetrans
ComponentsArginine deiminase
KeywordsHYDROLASE / arginine deiminase / L-arginine / L-citrulline / NH3
Function / homology
Function and homology information


arginine deiminase activity / arginine catabolic process
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 speciesMycoplasma penetrans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBenach, J. / Gallego, P. / Planell, R. / Querol, E. / Perez Pons, J.A. / Reverter, D.
CitationJournal: Plos One / Year: 2012
Title: Structural Characterization of the Enzymes Composing the Arginine Deiminase Pathway in Mycoplasma penetrans.
Authors: Gallego, P. / Planell, R. / Benach, J. / Querol, E. / Perez-Pons, J.A. / Reverter, D.
History
DepositionMar 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
C: Arginine deiminase
D: Arginine deiminase
E: Arginine deiminase
F: Arginine deiminase
G: Arginine deiminase
H: Arginine deiminase
I: Arginine deiminase
J: Arginine deiminase
K: Arginine deiminase
L: Arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)589,29524
Polymers588,86912
Non-polymers42512
Water29,0941615
1
A: Arginine deiminase
B: Arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2164
Polymers98,1452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-36 kcal/mol
Surface area30910 Å2
MethodPISA
2
C: Arginine deiminase
D: Arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2164
Polymers98,1452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-36 kcal/mol
Surface area30830 Å2
MethodPISA
3
E: Arginine deiminase
F: Arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2164
Polymers98,1452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-36 kcal/mol
Surface area30860 Å2
MethodPISA
4
G: Arginine deiminase
H: Arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2164
Polymers98,1452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-37 kcal/mol
Surface area30720 Å2
MethodPISA
5
I: Arginine deiminase
J: Arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2164
Polymers98,1452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-35 kcal/mol
Surface area30960 Å2
MethodPISA
6
K: Arginine deiminase
L: Arginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2164
Polymers98,1452
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-36 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.548, 128.875, 220.279
Angle α, β, γ (deg.)90.000, 91.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Arginine deiminase /


Mass: 49072.441 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma penetrans (bacteria) / Strain: HF-2 / Gene: MYPE6080 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8EVF6
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1615 / 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: 2.9 Å3/Da / Density % sol: 57.66 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 1.7 M Ammonium sulfate, pH 7 bis-tris 0.1M amb 15% glyOH, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 20, 2011
Details: (111) monochromator and Pt coated mirrors in a Kirkpatrick-Baez configuration
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 290893 / Num. obs: 290893 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rsym value: 0.06 / Net I/σ(I): 9.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.58 Å29.92 Å
Translation2.58 Å29.92 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8429 / σ(F): 1971
RfactorNum. reflection% reflection
Rfree0.2385 14608 4.9 %
Rwork0.2097 274281 -
obs-288889 96.9 %
Solvent computationBsol: 31.2009 Å2
Displacement parametersBiso max: 90.41 Å2 / Biso mean: 34.7898 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.937 Å20 Å2-1.039 Å2
2---5.811 Å20 Å2
3---4.874 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38004 0 12 1615 39631
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.325
X-RAY DIFFRACTIONc_mcbond_it1.2711.5
X-RAY DIFFRACTIONc_scbond_it1.9772
X-RAY DIFFRACTIONc_mcangle_it2.0872
X-RAY DIFFRACTIONc_scangle_it2.9312.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.380.331913990.3008266662806594.6
2.38-2.480.324614550.2804271892864496.3
2.48-2.590.303414860.2681271462863296.4
2.59-2.730.290514870.2519272282871596.7
2.73-2.90.286814720.2454273352880796.8
2.9-3.120.266314210.2321274772889897.1
3.12-3.430.253514650.2272275972906297.4
3.43-3.930.225814680.2004277112917997.7
3.93-4.950.187814360.1574278392927597.9
4.95-300.173615190.161280932961297.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top

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