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- PDB-4rhl: Crystal structure of T. brucei arginase-like protein triple mutan... -

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Basic information

Entry
Database: PDB / ID: 4rhl
TitleCrystal structure of T. brucei arginase-like protein triple mutant S149D/R151H/S226D bound with Mn2+
ComponentsArginase
KeywordsUNKNOWN FUNCTION / arginase-deacetylase fold
Function / homology
Function and homology information


putrescine biosynthetic process from arginine, via agmatine / agmatinase activity / arginine metabolic process / kinetoplast / arginase / arginase activity / mitochondrion / metal ion binding
Similarity search - Function
Ureohydrolase domain / Ureohydrolase / Arginase family / Arginase family profile. / Arginase; Chain A / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Arginase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHai, Y. / Barrett, M.P. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2015
Title: Crystal Structure of an Arginase-like Protein from Trypanosoma brucei That Evolved without a Binuclear Manganese Cluster.
Authors: Hai, Y. / Kerkhoven, E.J. / Barrett, M.P. / Christianson, D.W.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginase
B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8336
Polymers77,5382
Non-polymers2944
Water55831
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules

B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,49818
Polymers232,6156
Non-polymers88212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-y+2,x-y+3,z1
crystal symmetry operation3_475-x+y-1,-x+2,z1
crystal symmetry operation4_468y-1,x+1,-z+31
crystal symmetry operation5_688x-y+1,-y+3,-z+31
crystal symmetry operation6_668-x+1,-x+y+1,-z+31
Buried area17900 Å2
ΔGint-133 kcal/mol
Surface area65510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.582, 135.582, 86.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Arginase


Mass: 38769.223 Da / Num. of mol.: 2 / Mutation: S149D, R151H, S226D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.8.2020 / Production host: Escherichia coli (E. coli) / References: UniProt: Q581Y0, arginase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 20% (v/v) Jeffamine ED-2001, 0.1 M imidazole, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 16959 / Num. obs: 16959 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.1-3.211100
3.21-3.341100
3.34-3.491100
3.49-3.681100
3.68-3.911100
3.91-4.211100
4.21-4.631100
4.63-5.31100
5.3-6.671100
6.67-501100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RHK

4rhk


Resolution: 3.1→48.609 Å / SU ML: 0.36 / σ(F): 1.35 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 858 5.06 %random
Rwork0.2151 ---
obs0.218 16953 99.96 %-
all-16959 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4651 0 14 31 4696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044770
X-RAY DIFFRACTIONf_angle_d0.8246463
X-RAY DIFFRACTIONf_dihedral_angle_d14.3491775
X-RAY DIFFRACTIONf_chiral_restr0.032719
X-RAY DIFFRACTIONf_plane_restr0.004835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.29620.34741360.28082631X-RAY DIFFRACTION100
3.2962-3.55060.33141440.25632640X-RAY DIFFRACTION100
3.5506-3.90780.29191460.21372655X-RAY DIFFRACTION100
3.9078-4.47290.2451340.20072688X-RAY DIFFRACTION100
4.4729-5.63410.24031550.19752671X-RAY DIFFRACTION100
5.6341-48.61460.26561430.20142810X-RAY DIFFRACTION100

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