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- PDB-4rhi: Crystal structure of SeMet-labeled wild-type T. brucei arginase-l... -

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Basic information

Entry
Database: PDB / ID: 4rhi
TitleCrystal structure of SeMet-labeled wild-type T. brucei arginase-like protein in P321 space group
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 / SAD / Resolution: 2.55 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 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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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)78,9624
Polymers78,7782
Non-polymers1842
Water2,900161
1
A: Arginase
B: Arginase
hetero molecules

A: Arginase
B: Arginase
hetero molecules

A: Arginase
B: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,88512
Polymers236,3336
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area18790 Å2
ΔGint-101 kcal/mol
Surface area70800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.009, 139.009, 90.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21B-515-

HOH

31B-582-

HOH

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Components

#1: Protein Arginase


Mass: 39388.777 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M HEPES, pH 7.4, 10% PEG 3350, 5% 2-methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 33070 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.55-2.641100
2.64-2.751100
2.75-2.871100
2.87-3.021100
3.02-3.211100
3.21-3.461100
3.46-3.811100
3.81-4.361100
4.36-5.491100
5.49-50199.9

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Processing

Software
NameVersionClassification
CBASSdata collection
HKL2Mapmodel building
PHENIXmodel building
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→42.36 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 1672 5.06 %RANDOM
Rwork0.2208 ---
obs0.2228 33070 99.85 %-
all-33080 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 12 161 4984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034960
X-RAY DIFFRACTIONf_angle_d0.6286725
X-RAY DIFFRACTIONf_dihedral_angle_d12.5941861
X-RAY DIFFRACTIONf_chiral_restr0.024747
X-RAY DIFFRACTIONf_plane_restr0.004869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.62770.33771220.26052589X-RAY DIFFRACTION99
2.6277-2.71250.32451240.26792574X-RAY DIFFRACTION100
2.7125-2.80950.26331560.242575X-RAY DIFFRACTION100
2.8095-2.92190.2741410.23042592X-RAY DIFFRACTION100
2.9219-3.05490.27251440.23372575X-RAY DIFFRACTION100
3.0549-3.21590.34011350.24212621X-RAY DIFFRACTION100
3.2159-3.41730.28411660.22842567X-RAY DIFFRACTION100
3.4173-3.6810.25481340.21662628X-RAY DIFFRACTION100
3.681-4.05110.25111480.20742595X-RAY DIFFRACTION100
4.0511-4.63670.23581410.19722646X-RAY DIFFRACTION100
4.6367-5.83940.25561350.20932658X-RAY DIFFRACTION100
5.8394-42.36620.20911260.21722778X-RAY DIFFRACTION100

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