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- PDB-4hww: Crystal structure of human Arginase-1 complexed with inhibitor 9 -

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Basic information

Entry
Database: PDB / ID: 4hww
TitleCrystal structure of human Arginase-1 complexed with inhibitor 9
ComponentsArginase-1
KeywordsHydrolase/Hydrolase Inhibitor / metalloenzyme / alpha/beta fold / Hydrolase / Arginine metabolism / Manganese / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginine catabolic process to ornithine / arginase / arginase activity / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginine catabolic process to ornithine / arginase / arginase activity / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytosol / 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
: / Chem-X7A / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.298 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 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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_seq_id / _struct_conn.ptnr2_label_asym_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-1
B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6748
Polymers67,8482
Non-polymers8266
Water9,458525
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,01112
Polymers101,7723
Non-polymers1,2399
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area5530 Å2
ΔGint-19 kcal/mol
Surface area32740 Å2
MethodPISA
2
B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules

B: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,01112
Polymers101,7723
Non-polymers1,2399
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5470 Å2
ΔGint-18 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.143, 90.143, 69.328
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11B-635-

HOH

21B-671-

HOH

Detailsbiological assembly is a trimer generated from monomer A in the asymmetric unit by the operations: -x+y, -x, z-l; -y, x-y, z+1; or from monomer B in the asymmetric unit by the operations: -x+y, -x, z; -y, x-y, z

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Components

#1: Protein Arginase-1 / / Liver-type arginase / Type I arginase


Mass: 33923.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05089, arginase
#2: Chemical ChemComp-X7A / [(5R)-5-amino-5-carboxy-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-)


Mass: 303.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H28BN2O5
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Malonic Acid, Imidazol, Boric system, 25% Polyethylene Glycol (PEG) 1500, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91907
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2012
RadiationMonochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91907 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.48
ReflectionResolution: 1.298→50 Å / Num. all: 155548 / Num. obs: 155548 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.051 / Χ2: 1.026 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.354.30.591155621.009199.6
1.35-1.450.504154841199.8
1.4-1.465.10.369156321.012199.9
1.46-1.5450.244155221.0311100
1.54-1.644.70.166155701.041100
1.64-1.764.50.115155301.0511100
1.76-1.945.30.075156281.0331100
1.94-2.225.30.049155581.046199.9
2.22-2.85.10.036155721.0191100
2.8-504.90.024154901.021199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1D3V

1d3v


Resolution: 1.298→25.919 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8992 / Cross valid method: R-free / σ(F): 0 / Phase error: 17.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 7812 5.02 %Random 5%
Rwork0.1511 ---
all0.1585 155548 --
obs0.1585 155548 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 24.89 Å2 / Biso mean: 10.7663 Å2 / Biso min: 5.29 Å2
Refinement stepCycle: LAST / Resolution: 1.298→25.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 46 525 5345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074928
X-RAY DIFFRACTIONf_angle_d1.2746688
X-RAY DIFFRACTIONf_chiral_restr0.115770
X-RAY DIFFRACTIONf_plane_restr0.006854
X-RAY DIFFRACTIONf_dihedral_angle_d13.1461864
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 (%)
1.2978-1.32020.23564280.22367238766692
1.3202-1.34410.22393690.21517415778495
1.3441-1.370.21253920.21647405779795
1.37-1.39790.20193910.20377296768795
1.3979-1.42830.21854040.20767396780095
1.4283-1.46150.20363890.19587435782495
1.4615-1.4980.1973860.19367374776095
1.498-1.53850.18933790.18857383776295
1.5385-1.58370.18793760.1857476785295
1.5837-1.63480.18924020.17677334773695
1.6348-1.69320.20653950.17597397779295
1.6932-1.76090.18093880.17337386777495
1.7609-1.84090.18814050.17617404780995
1.8409-1.93780.19043880.17187383777195
1.9378-2.0590.17613960.16947389778595
2.059-2.21760.17884060.1657390779695
2.2176-2.440.16933790.14977408778795
2.44-2.79140.15783780.14277416779495
2.7914-3.51060.15693850.13337389777495
3.5106-15.84180.1513710.11797376774795

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