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- PDB-4ie3: Crystal structure of human Arginase-2 complexed with inhbitor 1o -

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Basic information

Entry
Database: PDB / ID: 4ie3
TitleCrystal structure of human Arginase-2 complexed with inhbitor 1o
ComponentsArginase-2, mitochondrial
KeywordsHydrolase/Hydrolase inhibitor / metalloenzyme / alpha/beta fold / Hydrolase / Arginine metabolism / Manganese / Mitochondrion / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of interleukin-13 production / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / Urea cycle / arginase ...negative regulation of chemokine (C-C motif) ligand 4 production / negative regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of defense response to bacterium / negative regulation of macrophage inflammatory protein 1 alpha production / negative regulation of type 2 immune response / negative regulation of interleukin-13 production / negative regulation of chemokine (C-C motif) ligand 5 production / regulation of interleukin-1 beta production / Urea cycle / arginase / arginase activity / : / urea cycle / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of interleukin-17 production / regulation of reactive oxygen species biosynthetic process / ureteric bud development / negative regulation of tumor necrosis factor production / striated muscle contraction / nitric oxide biosynthetic process / Mitochondrial protein degradation / positive regulation of cellular senescence / manganese ion binding / adaptive immune response / mitochondrial matrix / innate immune response / mitochondrion / cytoplasm
Similarity search - Function
Arginase / Ureohydrolase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1EE / BENZAMIDINE / BETA-MERCAPTOETHANOL / : / Arginase-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3522 Å
AuthorsCousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Beckett, P. / Van Zandt, M.C. / Ji, M.K. / Whitehouse, D. / Ryder, T. / Jagdmann, E. / Andreoli, M. ...Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Beckett, P. / Van Zandt, M.C. / Ji, M.K. / Whitehouse, D. / Ryder, T. / Jagdmann, E. / Andreoli, M. / Mazur, A. / Padmanilayam, M. / Schroeter, H. / Golebiowski, A. / Podjarny, A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: 2-Substituted-2-amino-6-boronohexanoic acids as arginase inhibitors.
Authors: Golebiowski, A. / Paul Beckett, R. / Van Zandt, M. / Ji, M.K. / Whitehouse, D. / Ryder, T.R. / Jagdmann, E. / Andreoli, M. / Mazur, A. / Padmanilayam, M. / Cousido-Siah, A. / Mitschler, A. / ...Authors: Golebiowski, A. / Paul Beckett, R. / Van Zandt, M. / Ji, M.K. / Whitehouse, D. / Ryder, T.R. / Jagdmann, E. / Andreoli, M. / Mazur, A. / Padmanilayam, M. / Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Podjarny, A. / Schroeter, H.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Dec 18, 2013Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Arginase-2, mitochondrial
B: Arginase-2, mitochondrial
C: Arginase-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,65519
Polymers99,6953
Non-polymers1,96016
Water11,241624
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Arginase-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8596
Polymers33,2321
Non-polymers6275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Arginase-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9377
Polymers33,2321
Non-polymers7056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Arginase-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8596
Polymers33,2321
Non-polymers6275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.086, 128.086, 159.079
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Arginase-2, mitochondrial / Kidney-type arginase / Non-hepatic arginase / Type II arginase


Mass: 33231.656 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG2 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P78540, arginase

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Non-polymers , 5 types, 640 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-1EE / [(5R)-5-amino-5-carboxy-7-(4-hydroxypiperidin-1-yl)heptyl](trihydroxy)borate(1-)


Mass: 319.182 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H28BN2O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals in condition H3 from Silver Bullet screen (Hampton Research) using Tacsimate in the reservoir, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 17, 2009 / Details: OSMIC MIRRORS
RadiationMonochromator: DOUBLE MIRRORS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 55026 / Num. obs: 55026 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rsym value: 0.103 / Net I/σ(I): 19.9
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 8.1 / Rsym value: 0.223 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1144refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D3V

1d3v


Resolution: 2.3522→25.963 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8734 / SU ML: 0.2 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 18.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1935 2788 5.08 %Random 5%
Rwork0.1464 ---
all0.1488 54928 --
obs0.1488 54928 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.62 Å2 / Biso mean: 22.5347 Å2 / Biso min: 5.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3522→25.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 115 624 7750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087424
X-RAY DIFFRACTIONf_angle_d1.29610137
X-RAY DIFFRACTIONf_chiral_restr0.1181163
X-RAY DIFFRACTIONf_plane_restr0.0051329
X-RAY DIFFRACTIONf_dihedral_angle_d13.4322767
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3522-2.39280.22841250.15592478260396
2.3928-2.43620.21641440.149925762720100
2.4362-2.48310.20871440.144926042748100
2.4831-2.53370.23071290.141825872716100
2.5337-2.58880.1911370.145325972734100
2.5888-2.64890.22011340.14725922726100
2.6489-2.71510.21571360.150626162752100
2.7151-2.78840.18781490.152326012750100
2.7884-2.87040.22731470.149625852732100
2.8704-2.96290.23981220.157626122734100
2.9629-3.06860.23721440.163426152759100
3.0686-3.19130.20641370.165826142751100
3.1913-3.33620.21181250.165626102735100
3.3362-3.51170.2311360.151826212757100
3.5117-3.73120.20131450.14592628277399
3.7312-4.01830.19221540.13752602275698
4.0183-4.42090.1421600.12492577273798
4.4209-5.05650.14781410.12052579272096
5.0565-6.35520.17721350.1472718285399
6.3552-25.96440.16781440.15282728287295

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