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- PDB-4i06: Crystal structure of human Arginase-2 complexed with inhibitor 14 -

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Basic information

Entry
Database: PDB / ID: 4i06
TitleCrystal structure of human Arginase-2 complexed with inhibitor 14
ComponentsArginase-2, mitochondrial
KeywordsHYDROLASE / metalloenzyme / alpha/beta fold / Arginine metabolism / Manganese / Mitochondrion
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-X8A / Arginase-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Whitehouse, D.L. / Golebiowski, A. / Ji, M. / Zhang, M. / Beckett, P. / Sheeler, R. / Andreoli, M. ...Cousido-Siah, A. / Mitschler, A. / Ruiz, F.X. / Whitehouse, D.L. / Golebiowski, A. / Ji, M. / Zhang, M. / Beckett, P. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / Schroeter, H. / Van Zandt, M.C. / Podjarny, A.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Discovery of (R)-2-Amino-6-borono-2-(2-(piperidin-1-yl)ethyl)hexanoic Acid and Congeners As Highly Potent Inhibitors of Human Arginases I and II for Treatment of Myocardial Reperfusion Injury.
Authors: Van Zandt, M.C. / Whitehouse, D.L. / Golebiowski, A. / Ji, M.K. / Zhang, M. / Beckett, R.P. / Jagdmann, G.E. / Ryder, T.R. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / ...Authors: Van Zandt, M.C. / Whitehouse, D.L. / Golebiowski, A. / Ji, M.K. / Zhang, M. / Beckett, R.P. / Jagdmann, G.E. / Ryder, T.R. / Sheeler, R. / Andreoli, M. / Conway, B. / Mahboubi, K. / D'Angelo, G. / Mitschler, A. / Cousido-Siah, A. / Ruiz, F.X. / Howard, E.I. / Podjarny, A.D. / Schroeter, H.
History
DepositionNov 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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)101,80521
Polymers99,6953
Non-polymers2,11118
Water18,2491013
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)33,9357
Polymers33,2321
Non-polymers7046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Arginase-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9357
Polymers33,2321
Non-polymers7046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Arginase-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9357
Polymers33,2321
Non-polymers7046
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.805, 127.805, 159.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

21C-592-

HOH

31C-732-

HOH

Detailsbiological assembly is a homotrimer with one copy in the asymmetric unit

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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, 1031 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.: 6 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-X8A / [(5R)-5-carboxy-5-(methylamino)-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)


Mass: 317.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30BN2O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1013 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.70849 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2012
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70849 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 121968 / Num. obs: 121968 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 21.27 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.8 / Num. unique all: 11993 / % possible all: 99.9

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Processing

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

1d3v


Resolution: 1.8→40.809 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.89 / SU ML: 0.15 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 6120 5.02 %Random 5%
Rwork0.1643 ---
all0.1658 121877 --
obs0.1658 121877 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.97 Å2 / Biso mean: 20.6535 Å2 / Biso min: 6.99 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 123 1013 8147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087462
X-RAY DIFFRACTIONf_angle_d1.35210188
X-RAY DIFFRACTIONf_chiral_restr0.1261164
X-RAY DIFFRACTIONf_plane_restr0.0061337
X-RAY DIFFRACTIONf_dihedral_angle_d13.2472797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7993-1.81980.27361950.234537723967100
1.8198-1.84120.26012280.220237934021100
1.8412-1.86370.27282350.209637613996100
1.8637-1.88720.24192100.205738054015100
1.8872-1.91210.23332080.192438354043100
1.9121-1.93830.21321890.189538184007100
1.9383-1.9660.22291900.185738544044100
1.966-1.99530.22751980.180838054003100
1.9953-2.02650.19862020.179137943996100
2.0265-2.05970.20232100.175538444054100
2.0597-2.09520.22572080.166938064014100
2.0952-2.13330.18831750.162738584033100
2.1333-2.17430.19571880.162538274015100
2.1743-2.21870.17911780.162438554033100
2.2187-2.2670.1781910.155938394030100
2.267-2.31970.20372260.157938404066100
2.3197-2.37770.19281880.153638494037100
2.3777-2.4420.1962100.153738294039100
2.442-2.51380.16792090.151638474056100
2.5138-2.5950.22822170.160238284045100
2.595-2.68770.19752210.169738294050100
2.6877-2.79530.1992000.166738734073100
2.7953-2.92250.20871930.172138794072100
2.9225-3.07650.22262030.170738834086100
3.0765-3.26920.19332180.173738764094100
3.2692-3.52140.19962040.154439034107100
3.5214-3.87560.19212120.148939184130100
3.8756-4.43580.14612070.141539574164100
4.4358-5.58640.1621900.145539954185100
5.5864-40.81950.19262170.17844185440299

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