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- PDB-6ksy: Crystal structure of arginase from Zymomonas mobilis ZM4 -

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Basic information

Entry
Database: PDB / ID: 6ksy
TitleCrystal structure of arginase from Zymomonas mobilis ZM4
ComponentsArginase/agmatinase/formiminoglutamase
KeywordsHYDROLASE / arginase
Function / homology
Function and homology information


: / arginase activity / manganese ion binding / cytosol
Similarity search - Function
Ureohydrolase domain / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Arginase/agmatinase/formiminoglutamase
Similarity search - Component
Biological speciesZymomonas mobilis subsp. mobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.649 Å
AuthorsPark, S.Y. / Hwangbo, S.A.
CitationJournal: Front Microbiol / Year: 2019
Title: Characterization of a Dimeric Arginase FromZymomonas mobilisZM4.
Authors: Hwangbo, S.A. / Kim, J.W. / Jung, S.J. / Jin, K.S. / Lee, J.O. / Kim, J.S. / Park, S.Y.
History
DepositionAug 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginase/agmatinase/formiminoglutamase
B: Arginase/agmatinase/formiminoglutamase
C: Arginase/agmatinase/formiminoglutamase
D: Arginase/agmatinase/formiminoglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,14212
Polymers128,6194
Non-polymers5238
Water14,556808
1
A: Arginase/agmatinase/formiminoglutamase
D: Arginase/agmatinase/formiminoglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5716
Polymers64,3092
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-44 kcal/mol
Surface area21780 Å2
MethodPISA
2
B: Arginase/agmatinase/formiminoglutamase
hetero molecules

C: Arginase/agmatinase/formiminoglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5716
Polymers64,3092
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area4400 Å2
ΔGint-41 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.107, 100.324, 79.600
Angle α, β, γ (deg.)90.000, 113.310, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Arginase/agmatinase/formiminoglutamase / Ureohydrolase-like protein


Mass: 32154.740 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria)
Strain: ATCC 31821 / ZM4 / CP4 / Gene: rocF, ZMO0432, ZMO1_ZMO0432 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NQE9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 46.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25 % (w/v) Polyethylene glycol 3350, 0.2 M Lithium Sulfate, 0.1 M Tris-HCl at pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2019 / Details: K-B
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.649→20 Å / Num. obs: 131592 / % possible obs: 95.2 % / Redundancy: 6.5 % / Rpim(I) all: 0.036 / Net I/σ(I): 17.6
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 6498 / Rpim(I) all: 0.388

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.649→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1877 1999 -
Rwork0.1652 --
obs-131527 94.84 %
Refinement stepCycle: LAST / Resolution: 1.649→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8958 0 8 808 9774
LS refinement shellResolution: 1.649→1.708 Å / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2395 --
Rwork0.2348 --
obs-12328 89.06 %

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