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- PDB-4rhq: Crystal structure of T. brucei arginase-like protein double mutan... -

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Basic information

Entry
Database: PDB / ID: 4rhq
TitleCrystal structure of T. brucei arginase-like protein double mutant S149D/S153D
ComponentsArginase
KeywordsUNKNOWN FUNCTION / arginase/deacetylase fold
Function / homology
Function and homology information


putrescine biosynthetic process from arginine, using agmatinase / agmatinase activity / arginine metabolic process / arginase / arginase activity / 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
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)116,7979
Polymers116,3653
Non-polymers4326
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-25 kcal/mol
Surface area34070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.184, 138.060, 90.937
Angle α, β, γ (deg.)90.00, 101.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-530-

HOH

21C-538-

HOH

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Components

#1: Protein Arginase


Mass: 38788.270 Da / Num. of mol.: 3 / Mutation: S149D, S153D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1 / Gene: Tb927.8.2020 / Plasmid: pET28(a)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q581Y0, arginase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M KF, 20% (v/v) PEG 3350, pH 8.5, 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: Apr 18, 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: 2.18→50 Å / Num. all: 51698 / Num. obs: 51646 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.18-2.26199.3
2.26-2.35199.9
2.35-2.461100
2.46-2.581100
2.58-2.751100
2.75-2.961100
2.96-3.261100
3.26-3.731100
3.73-4.71100
4.7-501100

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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: 2.18→44.479 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 2632 5.1 %random
Rwork0.2048 ---
obs0.2065 51633 98.99 %-
all-51646 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→44.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7091 0 28 163 7282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047294
X-RAY DIFFRACTIONf_angle_d0.6979882
X-RAY DIFFRACTIONf_dihedral_angle_d12.2092718
X-RAY DIFFRACTIONf_chiral_restr0.0331098
X-RAY DIFFRACTIONf_plane_restr0.0041279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.22090.36111350.29682102X-RAY DIFFRACTION82
2.2209-2.26360.341540.29342552X-RAY DIFFRACTION99
2.2636-2.30980.37291360.28162602X-RAY DIFFRACTION100
2.3098-2.360.28781470.26922583X-RAY DIFFRACTION100
2.36-2.41490.25351350.25592597X-RAY DIFFRACTION100
2.4149-2.47530.2631260.2332591X-RAY DIFFRACTION100
2.4753-2.54220.29621260.24122627X-RAY DIFFRACTION100
2.5422-2.6170.27321320.2382629X-RAY DIFFRACTION100
2.617-2.70150.26561390.23032576X-RAY DIFFRACTION100
2.7015-2.7980.27921410.2392607X-RAY DIFFRACTION100
2.798-2.910.28981470.23562596X-RAY DIFFRACTION100
2.91-3.04240.24841440.23972601X-RAY DIFFRACTION100
3.0424-3.20280.25051480.21842599X-RAY DIFFRACTION100
3.2028-3.40340.22811380.21172586X-RAY DIFFRACTION100
3.4034-3.66610.23271380.19982650X-RAY DIFFRACTION100
3.6661-4.03480.20611210.16982596X-RAY DIFFRACTION100
4.0348-4.61810.1911240.15662632X-RAY DIFFRACTION100
4.6181-5.81630.18591600.15792617X-RAY DIFFRACTION100
5.8163-44.48810.17241410.1582658X-RAY DIFFRACTION100

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