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- PDB-4hze: Crystal structure of human Arginase-2 complexed with inhibitor 9 -

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Basic information

Entry
Database: PDB / ID: 4hze
TitleCrystal structure of human Arginase-2 complexed with inhibitor 9
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 macrophage inflammatory protein 1 alpha production / negative regulation of defense response to bacterium / 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 macrophage inflammatory protein 1 alpha production / negative regulation of defense response to bacterium / 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 / arginine catabolic process to ornithine / 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
Ureohydrolase domain / Arginase / 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-X7A / Arginase-2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.602 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 15, 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)101,76321
Polymers99,6953
Non-polymers2,06818
Water18,7721042
1


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


Theoretical massNumber of molelcules
Total (without water)33,9217
Polymers33,2321
Non-polymers6896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Arginase-2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9217
Polymers33,2321
Non-polymers6896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.736, 127.736, 159.111
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-680-

HOH

21C-593-

HOH

31C-739-

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, 1060 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-X7A / [(5R)-5-amino-5-carboxy-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)


Mass: 303.183 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H28BN2O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 62.21 %
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: X06DA / Wavelength: 0.92019 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2011
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92019 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 166624 / Num. obs: 166624 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 16.42 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.156
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 3.439 / Num. unique all: 16450 / % possible all: 96.7

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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: 1.602→48.983 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.8857 / SU ML: 0.14 / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Phase error: 18.31 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 8478 5.09 %Random 5%
Rwork0.1744 ---
all0.1756 166505 --
obs0.1756 166505 96.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.34 Å2 / Biso mean: 20.0344 Å2 / Biso min: 6.81 Å2
Refinement stepCycle: LAST / Resolution: 1.602→48.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 120 1042 8173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097447
X-RAY DIFFRACTIONf_angle_d1.35410164
X-RAY DIFFRACTIONf_chiral_restr0.1311164
X-RAY DIFFRACTIONf_plane_restr0.0071331
X-RAY DIFFRACTIONf_dihedral_angle_d13.4142803
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 (%)
1.6016-1.61980.22762760.20955087536395
1.6198-1.63890.23042980.21485176547497
1.6389-1.65890.25322770.21385266554397
1.6589-1.67990.20393300.20295181551198
1.6799-1.7020.21092740.19415309558398
1.702-1.72530.21972790.19075292557199
1.7253-1.74990.22442820.19625359564199
1.7499-1.77610.22742760.19885339561599
1.7761-1.80380.24812880.201353665654100
1.8038-1.83340.2252830.19185330561399
1.8334-1.8650.19312860.180453955681100
1.865-1.89890.20412740.183753985672100
1.8989-1.93540.21733110.18425294560598
1.9354-1.97490.20212880.17785250553898
1.9749-2.01790.212900.17955407569799
2.0179-2.06480.19923090.178653805689100
2.0648-2.11650.19912880.17165366565499
2.1165-2.17370.20132850.16875376566199
2.1737-2.23770.18532940.16735380567499
2.2377-2.30990.19772720.16575361563399
2.3099-2.39240.20542710.16315388565999
2.3924-2.48820.18832750.16985407568299
2.4882-2.60150.18122710.16465371564298
2.6015-2.73860.21023210.17285322564398
2.7386-2.91020.20142520.17255379563197
2.9102-3.13480.19613060.18025267557396
3.1348-3.45020.18422610.16845152541393
3.4502-3.94930.18842430.16244670491384
3.9493-4.97490.17522400.15424372461278
4.9749-49.00550.18552780.17785387566592

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