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- PDB-4rhj: Crystal structure of wild-type T. brucei arginase-like protein in... -

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Basic information

Entry
Database: PDB / ID: 4rhj
TitleCrystal structure of wild-type T. brucei arginase-like protein in a reduced form
ComponentsArginase
KeywordsUNKNOWN FUNCTION / Arginase-deacetylase fold
Function / homology
Function and homology information


putrescine biosynthetic process from arginine, via agmatine / 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: 1.8 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
D: Arginase
E: Arginase
F: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,64210
Polymers232,3946
Non-polymers2484
Water5,477304
1
A: Arginase
hetero molecules

A: Arginase
hetero molecules

A: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3836
Polymers116,1973
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6170 Å2
ΔGint-16 kcal/mol
Surface area35120 Å2
MethodPISA
2
B: Arginase

B: Arginase

B: Arginase


Theoretical massNumber of molelcules
Total (without water)116,1973
Polymers116,1973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5640 Å2
ΔGint-25 kcal/mol
Surface area34820 Å2
MethodPISA
3
C: Arginase
hetero molecules

C: Arginase
hetero molecules

C: Arginase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,75512
Polymers116,1973
Non-polymers5599
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area7200 Å2
ΔGint-10 kcal/mol
Surface area35100 Å2
MethodPISA
4
D: Arginase

D: Arginase

D: Arginase


Theoretical massNumber of molelcules
Total (without water)116,1973
Polymers116,1973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area5850 Å2
ΔGint-26 kcal/mol
Surface area34630 Å2
MethodPISA
5
E: Arginase

E: Arginase

E: Arginase


Theoretical massNumber of molelcules
Total (without water)116,1973
Polymers116,1973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6170 Å2
ΔGint-20 kcal/mol
Surface area33930 Å2
MethodPISA
6
F: Arginase

F: Arginase

F: Arginase


Theoretical massNumber of molelcules
Total (without water)116,1973
Polymers116,1973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5700 Å2
ΔGint-30 kcal/mol
Surface area34070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.243, 139.243, 90.167
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

21C-512-

HOH

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Components

#1: Protein
Arginase


Mass: 38732.250 Da / Num. of mol.: 6
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.17 Å3/Da / Density % sol: 43.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1 M HEPES, pH 7.8, 18% PEG 3350, 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: Jul 23, 2014
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.49
ReflectionResolution: 1.8→50 Å / Num. all: 181427 / Num. obs: 181427 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.8-1.861100
1.86-1.941100
1.94-2.031100
2.03-2.131100
2.13-2.271100
2.27-2.441100
2.44-2.691100
2.69-3.081100
3.08-3.881100
3.88-501100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4RHI

4rhi


Resolution: 1.8→42.229 Å / σ(F): 1.97 / Phase error: 24.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 9089 5.01 %random
Rwork0.1964 ---
obs0.2023 181427 100 %-
all-181427 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→42.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13287 0 16 304 13607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913640
X-RAY DIFFRACTIONf_angle_d1.18218496
X-RAY DIFFRACTIONf_dihedral_angle_d15.5735112
X-RAY DIFFRACTIONf_chiral_restr0.0482067
X-RAY DIFFRACTIONf_plane_restr0.0062401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.83050.32714610.29368566X-RAY DIFFRACTION95
1.8305-1.86380.31944680.27638643X-RAY DIFFRACTION95
1.8638-1.89960.31094500.27618587X-RAY DIFFRACTION95
1.8996-1.93840.30134760.26168605X-RAY DIFFRACTION95
1.9384-1.98050.26554590.2418650X-RAY DIFFRACTION95
1.9805-2.02660.27544470.23688594X-RAY DIFFRACTION95
2.0266-2.07730.28964480.22928661X-RAY DIFFRACTION95
2.0773-2.13340.26514710.22378569X-RAY DIFFRACTION95
2.1334-2.19620.25334370.22228611X-RAY DIFFRACTION95
2.1962-2.26710.23994240.21668632X-RAY DIFFRACTION95
2.2671-2.34810.2354650.21318619X-RAY DIFFRACTION95
2.3481-2.44210.25384420.2138703X-RAY DIFFRACTION95
2.4421-2.55320.25894520.20928576X-RAY DIFFRACTION95
2.5532-2.68780.22744670.20368578X-RAY DIFFRACTION95
2.6878-2.85620.22524670.20168612X-RAY DIFFRACTION95
2.8562-3.07670.23964290.19338646X-RAY DIFFRACTION95
3.0767-3.38610.21614410.1828668X-RAY DIFFRACTION95
3.3861-3.87580.21474640.16748566X-RAY DIFFRACTION95
3.8758-4.88180.20374670.15868606X-RAY DIFFRACTION95
4.8818-40.68690.22734540.19188632X-RAY DIFFRACTION95

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