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- PDB-6q37: Complex of Arginase 2 with Example 23 -

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Basic information

Entry
Database: PDB / ID: 6q37
TitleComplex of Arginase 2 with Example 23
ComponentsArginase-2, mitochondrial
KeywordsHYDROLASE / METALLOENZYME / ALPHA/BETA FOLD / 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
BENZAMIDINE / BETA-MERCAPTOETHANOL / Chem-HE8 / : / Arginase-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.211 Å
AuthorsPodjarny, A.D. / Van Zandt, M.C. / Cousido-Siah, A.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery ofN-Substituted 3-Amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic Acids as Highly Potent Third-Generation Inhibitors of Human Arginase I and II.
Authors: Van Zandt, M.C. / Jagdmann, G.E. / Whitehouse, D.L. / Ji, M. / Savoy, J. / Potapova, O. / Cousido-Siah, A. / Mitschler, A. / Howard, E.I. / Pyle, A.M. / Podjarny, A.D.
History
DepositionDec 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)101,38119
Polymers99,6953
Non-polymers1,68616
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint1 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.162, 128.162, 158.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-790-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Arginase-2, mitochondrial / Arginase II / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P78540, arginase

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Non-polymers , 6 types, 840 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.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-HE8 / 3-[(3~{S},4~{R})-4-azanyl-4-carboxy-pyrrolidin-3-yl]propyl-tris(oxidanyl)boranuide


Mass: 233.050 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18BN2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 62.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS IN CONDITION H3 FROM SILVER BULLET SCREEN (HAMPTON RESEARCH) USING TACSIMATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 20, 2010 / 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: 2.2→50 Å / Num. obs: 63343 / % possible obs: 93.8 % / Redundancy: 11.8 % / Biso Wilson estimate: 26.29 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Χ2: 1.037 / Net I/σ(I): 30.7 / Num. measured all: 747806
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 7066 / Rsym value: 0.285 / Χ2: 1.017 / % possible all: 60.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D3V

1d3v


Resolution: 2.211→26.496 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 3198 5.07 %
Rwork0.1482 59902 -
obs0.1503 63100 94.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.88 Å2 / Biso mean: 30.0241 Å2 / Biso min: 10.61 Å2
Refinement stepCycle: final / Resolution: 2.211→26.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 97 846 7953
Biso mean--26.89 41.97 -
Num. residues----918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087417
X-RAY DIFFRACTIONf_angle_d1.06810131
X-RAY DIFFRACTIONf_chiral_restr0.1081161
X-RAY DIFFRACTIONf_plane_restr0.0051332
X-RAY DIFFRACTIONf_dihedral_angle_d19.2622762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2112-2.24420.2504910.17021801189266
2.2442-2.27920.25791080.15881980208874
2.2792-2.31650.22071100.15792318242885
2.3165-2.35650.22671550.14572586274196
2.3565-2.39930.19971370.14562623276097
2.3993-2.44540.18891520.14762627277997
2.4454-2.49530.22161430.14692619276297
2.4953-2.54950.1751250.14852654277997
2.5495-2.60880.24351560.16262624278097
2.6088-2.67390.21731620.16022654281698
2.6739-2.74620.20191360.15652638277497
2.7462-2.82690.22071200.16242680280098
2.8269-2.9180.2141380.16222692283098
2.918-3.02220.21521480.16842657280598
3.0222-3.1430.21221630.16712679284298
3.143-3.28580.15981310.15532691282298
3.2858-3.45870.18631560.14672693284998
3.4587-3.67480.15961340.14052703283798
3.6748-3.95770.16841420.12962729287198
3.9577-4.35440.1541500.12392725287598
4.3544-4.98090.15841430.12092771291498
4.9809-6.26170.20551380.15732814295299
6.2617-26.49760.17591600.1622944310498

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