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- PDB-1t5f: arginase I-AOH complex -

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Basic information

Entry
Database: PDB / ID: 1t5f
Titlearginase I-AOH complex
ComponentsArginase 1
KeywordsHYDROLASE / arginase / AOH
Function / homology
Function and homology information


regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / arginine metabolic process / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / : ...regulation of L-arginine import across plasma membrane / Urea cycle / collagen biosynthetic process / mammary gland involution / arginine metabolic process / positive regulation of neutrophil mediated killing of fungus / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / : / response to selenium ion / urea cycle / response to methylmercury / response to vitamin A / response to nematode / response to manganese ion / response to steroid hormone / response to herbicide / Neutrophil degranulation / response to zinc ion / response to vitamin E / negative regulation of type II interferon-mediated signaling pathway / response to amine / defense response to protozoan / negative regulation of activated T cell proliferation / response to amino acid / maternal process involved in female pregnancy / response to axon injury / cellular response to transforming growth factor beta stimulus / response to cadmium ion / negative regulation of T cell proliferation / positive regulation of endothelial cell proliferation / cellular response to dexamethasone stimulus / cellular response to glucagon stimulus / cellular response to interleukin-4 / female pregnancy / liver development / lung development / 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 / 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
(S)-2-AMINO-7,7-DIHYDROXYHEPTANOIC ACID / : / Arginase-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShin, H. / Cama, E. / Christianson, D.W.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Design of amino acid aldehydes as transition-state analogue inhibitors of arginase
Authors: Shin, H. / Cama, E. / Christianson, D.W.
History
DepositionMay 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: 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.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

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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)102,40112
Polymers101,5403
Non-polymers8619
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-57 kcal/mol
Surface area33830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.900, 87.900, 105.200
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: 33846.617 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: ARG1 / Cell line (production host): BL21(DE3) / 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-DHH / (S)-2-AMINO-7,7-DIHYDROXYHEPTANOIC ACID


Mass: 177.198 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H15NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: bicine, PEG8000, AOH, 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: Oct 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 43716 / Num. obs: 43716 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.3 Å2
Reflection shellResolution: 2.2→2.3 Å / % possible all: 85.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1913177 / 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
Rfree0.241 2099 5 %RANDOM
Rwork0.222 ---
all0.222 41783 --
obs0.222 41783 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4624 Å2 / ksol: 0.360029 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.33 Å20.98 Å20 Å2
2---2.33 Å20 Å2
3---4.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7155 0 42 245 7442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.432.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 300 5.3 %
Rwork0.352 5337 -
obs--73.7 %
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 DIFFRACTION4UNK2.PARUNK2.TOP

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