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- PDB-3mfv: Crystal structure of human arginase I in complex with 2-aminohomo... -

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Basic information

Entry
Database: PDB / ID: 3mfv
TitleCrystal structure of human arginase I in complex with 2-aminohomohistidine
ComponentsArginase-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Manganese coordination / structure based design / inhibition / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan ...positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / Urea cycle / arginase / arginase activity / : / urea cycle / response to nematode / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / L-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
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-Z70 / Arginase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDi Costanzo, L. / Christianson, D.W.
CitationJournal: J.Med.Chem. / Year: 2010
Title: 2-aminoimidazole amino acids as inhibitors of the binuclear manganese metalloenzyme human arginase I.
Authors: Ilies, M. / Di Costanzo, L. / North, M.L. / Scott, J.A. / Christianson, D.W.
History
DepositionApr 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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.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-1
B: Arginase-1
A: (2S)-2-amino-4-(2-amino-1H-imidazol-5-yl)butanoic acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1488
Polymers69,5602
Non-polymers5886
Water6,125340
1
A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules

A: Arginase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,22212
Polymers104,3403
Non-polymers8829
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 area5630 Å2
ΔGint-18 kcal/mol
Surface area32650 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)105,22212
Polymers104,3403
Non-polymers8829
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 area5470 Å2
ΔGint-16 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.660, 90.660, 69.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-496-

HOH

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Components

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


Mass: 34779.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Plasmid: pET11-d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P05089, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-Z70 / (2S)-2-amino-4-(2-amino-1H-imidazol-5-yl)butanoic acid / 2-aminohomohistidine


Type: L-peptide linking / Mass: 184.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 3 uL of protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM AHH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 28% Jeffamine] were equilibrated against a ...Details: 3 uL of protein solution [3.5 mg/mL protein, 50 mM bicine (pH 8.5), 2 mM AHH, 100 M MnCl2] and 3 uL of precipitant solution [0.1 M HEPES (pH 7.0), 28% Jeffamine] were equilibrated against a 1 mL reservoir of precipitant solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 50344 / Num. obs: 50344 / % possible obs: 99.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 15.4
Reflection shellResolution: 1.9→1.99 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.31 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZAV

2zav


Resolution: 1.9→50 Å
Details: THE STRUCTURE IS AFFECTED BY PERFECT HEMIHEDRAL TWINNING. DATA HAVE BEEN USED WITH NO PRIOR DETWINNING. TWIN LAW: -H,-K,L; TWIN FRACTION=0.5
RfactorNum. reflection
Rfree0.19 2184
Rwork0.141 -
obs0.141 49288
all-49288
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4762 0 30 340 5132
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg2.1

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