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- PDB-3rla: ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES T... -

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Basic information

Entry
Database: PDB / ID: 3rla
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 / arginine metabolic process / negative regulation of T-helper 2 cell cytokine production / response to selenium ion / arginase / arginine catabolic process to ornithine ...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 / arginase / arginine catabolic process to ornithine / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.54 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_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 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: 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)105,3159
Polymers104,9853
Non-polymers3306
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-60 kcal/mol
Surface area34460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.000, 89.000, 115.400
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(-0.420945, -0.852193, 0.310761), (0.844137, -0.493426, -0.209675), (0.332021, 0.174063, 0.927073)-0.01375, 51.70329, 0.59379
2given(-0.439303, 0.845288, 0.304141), (-0.847093, -0.502493, 0.173016), (0.299077, -0.18163, 0.936784)-44.10607, 25.85707, 9.31568

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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.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13-4 mg/mlenzyme1drop
250 mMBicine1drop
37-8 %PEG80001drop
40.025 %sodium azide1drop
50.5 mM1dropMnCl2
650 mMBicine1reservoir
714-16 %PEG80001reservoir
80.05 %sodium azide1reservoir
91 mM1reservoirMnCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / 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: 2.5→8 Å / Num. obs: 26381 / % possible obs: 74 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 4.3
Reflection shellResolution: 2.54→2.6 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.4 / % possible all: 79.5
Reflection
*PLUS
Num. measured all: 65410

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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: 2.54→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
Rfree0.282 694 3 %RANDOM
Rwork0.194 ---
obs0.194 24212 74 %-
Refine analyzeLuzzati d res low obs: 12 Å / Luzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.54→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 1 20 3251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_d24.3
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: 2.54→2.65 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.5 102 2.4 %
Rwork0.42 3245 -
obs--79.5 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor Rfree: 0.5

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