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- PDB-1rla: THREE-DIMENSIONAL STRUCTURE OF RAT LIVER ARGINASE, THE BINUCLEAR ... -

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Basic information

Entry
Database: PDB / ID: 1rla
TitleTHREE-DIMENSIONAL STRUCTURE OF RAT LIVER ARGINASE, THE BINUCLEAR MANGANESE METALLOENZYME OF THE UREA CYCLE
ComponentsARGINASE
KeywordsHYDROLASE / UREA CYCLE / ARGININE METABOLISM / MAGNESIUM
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 / arginine metabolic process / negative regulation of T-helper 2 cell cytokine production / response to selenium ion / response to methylmercury / 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 / arginine metabolic process / negative regulation of T-helper 2 cell cytokine production / response to selenium ion / response to methylmercury / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / response to manganese ion / response to vitamin A / response to steroid hormone / Neutrophil degranulation / response to herbicide / response to zinc ion / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / response to amine / negative regulation of activated T cell proliferation / response to axon injury / response to vitamin E / response to amino acid / maternal process involved in female pregnancy / cellular response to interleukin-4 / response to cadmium ion / negative regulation of T cell proliferation / cellular response to transforming growth factor beta stimulus / cellular response to glucagon stimulus / 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 / adaptive immune response / response to lipopolysaccharide / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsKanyo, Z. / Scolnick, L. / Ash, D. / Christianson, D.W.
Citation
Journal: Nature / Year: 1996
Title: Structure of a unique binuclear manganese cluster in arginase.
Authors: Kanyo, Z.F. / Scolnick, L.R. / Ash, D.E. / Christianson, D.W.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystallization and Oligomeric Structure of Rat Liver Arginase
Authors: Kanyo, Z.F. / Chen, C.Y. / Daghigh, F. / Ash, D.E. / Christianson, D.W.
History
DepositionAug 15, 1996Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 30, 2020Group: Derived calculations / Other / Structure summary
Category: audit_author / pdbx_database_status ...audit_author / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.name / _pdbx_database_status.process_site ..._audit_author.name / _pdbx_database_status.process_site / _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
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGINASE
B: ARGINASE
C: ARGINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3879
Polymers105,0573
Non-polymers3306
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-58 kcal/mol
Surface area34190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.500, 88.500, 106.200
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


Mass: 35019.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: PH 8.5 / Source: (natural) Rattus norvegicus (Norway rat) / Organ: LIVER / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop / Details: Kanyo, Z.F., (1992) J.Mol.Biol., 224, 1175.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
250 mMBicine1drop
31 mM1dropMnCl2
414 %(w/v)PEG80001reservoir
550 mMBicine1reservoir
61 mM1reservoirMnCl2
70.05 %(w/v)sodium azide1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 17, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.056
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 46162 / % possible obs: 91.6 % / Num. measured all: 147454
Reflection shell
*PLUS
% possible obs: 58.3 % / Rmerge(I) obs: 0.365

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2.1→20 Å / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.178 / Rfactor obs: 0.178 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7182 0 6 232 7420
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 47913
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_deg1.6

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