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- PDB-1t5g: Arginase-F2-L-Arginine complex -

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Basic information

Entry
Database: PDB / ID: 1t5g
TitleArginase-F2-L-Arginine complex
ComponentsArginase 1Arginase
KeywordsHYDROLASE / arginase / L-arginine / fluoride ions
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 / arginine catabolic process to ornithine / response to selenium ion / arginase ...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 / arginine catabolic process to ornithine / response to selenium ion / arginase / arginase activity / urea cycle / response to methylmercury / response to vitamin A / response to herbicide / response to steroid hormone / response to manganese ion / Neutrophil degranulation / response to zinc ion / negative regulation of type II interferon-mediated signaling pathway / cellular response to glucagon stimulus / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / maternal process involved in female pregnancy / response to axon injury / response to vitamin E / response to amino acid / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / cellular response to interleukin-4 / positive regulation of endothelial cell proliferation / cellular response to dexamethasone stimulus / liver development / female pregnancy / lung development / response to peptide hormone / cellular response to hydrogen peroxide / manganese ion binding / cellular response to lipopolysaccharide / mitochondrial outer membrane / response to lipopolysaccharide / adaptive immune response / response to xenobiotic stimulus / innate immune response / neuronal cell body / extracellular space / identical protein binding / 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
ARGININE / FLUORIDE ION / : / Arginase-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCama, E. / Pethe, S. / Boucher, J.-L. / Han, S. / Emig, F.A. / Ash, D.E. / Viola, R.E. / Mansuy, D. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2004
Title: Inhibitor coordination interactions in the binuclear manganese cluster of arginase
Authors: Cama, E. / Pethe, S. / Boucher, J.-L. / Han, S. / Emig, F.A. / Ash, D.E. / Viola, R.E. / Mansuy, D. / Christianson, D.W.
History
DepositionMay 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)102,50918
Polymers101,5403
Non-polymers96915
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-42 kcal/mol
Surface area33110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.720, 87.720, 104.520
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 / Arginase / Liver-type arginase


Mass: 33846.617 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-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: F
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: bicine, PEG8000, L-arginine, NaF, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.982 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 40418 / Num. obs: 40418 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.1 Å2
Reflection shellResolution: 2.4→2.5 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→27.69 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1201617.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1809 4.9 %RANDOM
Rwork0.228 ---
all0.228 35725 --
obs0.228 35725 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4624 Å2 / ksol: 0.360029 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.18 Å22.9 Å20 Å2
2---6.18 Å20 Å2
3---12.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.4→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7152 0 48 100 7300
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.071.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.32
X-RAY DIFFRACTIONc_scangle_it1.982.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.4→2.58 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 152 4.8 %
Rwork0.304 3023 -
obs--86.5 %
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 DIFFRACTION4SUB.PARSUB.TOP

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