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- PDB-1r1o: Amino Acid Sulfonamides as Transition-State Analogue Inhibitors o... -

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Basic information

Entry
Database: PDB / ID: 1r1o
TitleAmino Acid Sulfonamides as Transition-State Analogue Inhibitors of Arginase
ComponentsArginase 1
KeywordsHYDROLASE / arginase / sulfonamides / transition-state analogue
Function / homology
Function and homology information


regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginine metabolic process / arginase / : / arginase activity ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginine metabolic process / arginase / : / arginase activity / response to selenium ion / urea cycle / response to methylmercury / response to nematode / response to manganese ion / response to vitamin A / response to steroid hormone / response to herbicide / Neutrophil degranulation / response to zinc ion / response to vitamin E / defense response to protozoan / response to amine / negative regulation of type II interferon-mediated signaling pathway / negative regulation of activated T cell proliferation / maternal process involved in female pregnancy / cellular response to dexamethasone stimulus / response to cadmium ion / response to amino acid / cellular response to transforming growth factor beta stimulus / response to axon injury / negative regulation of T cell proliferation / positive regulation of endothelial cell proliferation / cellular response to glucagon stimulus / cellular response to interleukin-4 / lung development / liver development / female pregnancy / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / cellular response to lipopolysaccharide / response to lipopolysaccharide / adaptive immune response / mitochondrial outer membrane / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / cytoplasm / cytosol
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
: / S-[2-(AMINOSULFONYL)ETHYL]-D-CYSTEINE / Arginase-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCama, E. / Shin, H. / Christianson, D.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Design of Amino Acid Sulfonamides as Transition-State Analogue Inhibitors of Arginase
Authors: Cama, E. / Shin, H. / Christianson, D.W.
History
DepositionSep 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_conn.ptnr2_label_seq_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
C: Arginase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,07212
Polymers105,0573
Non-polymers1,0149
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-68 kcal/mol
Surface area33580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.940, 88.940, 112.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Arginase 1 / Liver-type arginase


Mass: 35019.098 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: ARG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07824, arginase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SDC / S-[2-(AMINOSULFONYL)ETHYL]-D-CYSTEINE


Mass: 228.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12N2O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, bicine, manganese chloride, SDC, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112-16 mg/mlarginase1drop
250 mMN,N-bis(2-hydroxyethyl)-glycine1droppH8.5
35 mM1dropMnCl2
45 mMSEC1drop
520 %PEG80001reservoir
650 mMBicine1reservoirpH8.1
75 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.916 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 17, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 23105 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.9 Å / % possible all: 82.5
Reflection
*PLUS
Num. measured all: 204073 / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 82.5 % / Rmerge(I) obs: 0.287

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 2099 RANDOM
Rwork0.251 --
obs0.251 21136 -
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a1.15 Å1.02 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7185 0 45 41 7271
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_dihedral_angle_d23.2
X-RAY DIFFRACTIONo_improper_angle_d1.13
X-RAY DIFFRACTIONo_mcbond_it3.531.5
X-RAY DIFFRACTIONo_mcangle_it5.692
X-RAY DIFFRACTIONo_scbond_it3.982
X-RAY DIFFRACTIONo_scangle_it6.192.5
Refine LS restraints NCSNCS model details: CONSTR
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4CISPEP2.PARAM
X-RAY DIFFRACTION5STEREO.PARAMSTEREO.TOP
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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