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- PDB-5rla: ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES T... -

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Basic information

Entry
Database: PDB / ID: 5rla
TitleALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION
ComponentsARGINASE
KeywordsHYDROLASE / UREA CYCLE / ARGININE METABOLISM
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 / 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
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsScolnick, L.R. / Kanyo, Z.F. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 1997
Title: Altering the binuclear manganese cluster of arginase diminishes thermostability and catalytic function.
Authors: Scolnick, L.R. / Kanyo, Z.F. / Cavalli, R.C. / Ash, D.E. / Christianson, D.W.
History
DepositionMay 7, 1997Processing site: BNL
Revision 1.0May 13, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_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_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_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)105,1506
Polymers104,9853
Non-polymers1653
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-42 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.900, 88.900, 105.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.50079, -0.860961, -0.089199), (0.85138, -0.471375, -0.230127), (0.156085, -0.191187, 0.969064)88.3822, -51.22077, -9.23558
2given(-0.509277, 0.837838, 0.196635), (-0.858407, -0.47823, -0.185563), (-0.061436, -0.263296, 0.962757)90.3287, 50.06401, 3.83133

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Components

#1: Protein ARGINASE


Mass: 34995.051 Da / Num. of mol.: 3 / Mutation: H101N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: PARGR-2 / Organ: LIVER / Plasmid: PRSET C / Species (production host): Escherichia coli / Gene (production host): PARG-X / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P07824, arginase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.5
Details: 12 - 18% PEG 8000, 50 MM BICINE PH = 8.5, 0.05% AZIDE, 1 MM MNCL2 SOAKED FOR 1 WEEK IN 15MM EDTA + DPA
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
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

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: YALE
RadiationMonochromator: YALE MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 37872 / % possible obs: 91.8 % / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 5.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.45 / % possible all: 94.9
Reflection
*PLUS
Num. obs: 23414 / Num. measured all: 37872
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RAT LIVER ARGINASE

Resolution: 2.74→15 Å / Rfactor Rfree error: 0.0004 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION USED
RfactorNum. reflection% reflectionSelection details
Rfree0.27 637 3 %RANDOM
Rwork0.175 ---
obs0.175 23414 91.8 %-
Refine analyzeLuzzati d res low obs: 12 Å / Luzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.74→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 1 27 3258
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.74→2.86 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.46 83 2.9 %
Rwork0.4 2640 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM-LRS.MAY96TOPH-LRS.MAY96
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 22421
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor obs: 0.4

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