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- PDB-4rhm: Crystal structure of T. brucei arginase-like protein quadruple mu... -

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Basic information

Entry
Database: PDB / ID: 4rhm
TitleCrystal structure of T. brucei arginase-like protein quadruple mutant S149D/R151H/S153D/S226D
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
: / Arginase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.95 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_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

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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)117,29515
Polymers116,3923
Non-polymers90412
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-49 kcal/mol
Surface area33370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.123, 137.350, 87.778
Angle α, β, γ (deg.)90.00, 102.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

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Components

#1: Protein Arginase


Mass: 38797.230 Da / Num. of mol.: 3 / Mutation: S149D, R151H, S153D, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M KNO3, 20% 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: 1.95→50 Å / Num. all: 68553 / Num. obs: 64646 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 17.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.95-2.01173.4
2.01-2.08180.9
2.08-2.17188.4
2.17-2.27196.1
2.27-2.39199.4
2.39-2.54199.6
2.54-2.73199.7
2.73-3.01199.9
3.01-3.441100
3.44-4.341100
4.34-50199.8

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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: PHASER
Starting model: PDB ENTRY 4RHK

4rhk


Resolution: 1.95→42.88 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 32.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 3247 5.03 %
Rwork0.201 --
obs0.203 64546 94 %
all-64646 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7076 0 51 129 7256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047289
X-RAY DIFFRACTIONf_angle_d0.7789874
X-RAY DIFFRACTIONf_dihedral_angle_d12.562707
X-RAY DIFFRACTIONf_chiral_restr0.031096
X-RAY DIFFRACTIONf_plane_restr0.0041275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98260.34661070.31611920X-RAY DIFFRACTION69
1.9826-2.01360.33241210.30982086X-RAY DIFFRACTION74
2.0136-2.04660.37531170.32273X-RAY DIFFRACTION79
2.0466-2.08190.34981190.28922300X-RAY DIFFRACTION82
2.0819-2.11970.32541220.28482408X-RAY DIFFRACTION85
2.1197-2.16050.32781340.28162514X-RAY DIFFRACTION89
2.1605-2.20460.29781550.28572598X-RAY DIFFRACTION93
2.2046-2.25250.31881300.2712735X-RAY DIFFRACTION96
2.2525-2.30490.33911470.24992793X-RAY DIFFRACTION99
2.3049-2.36260.27311400.23982834X-RAY DIFFRACTION99
2.3626-2.42640.24931570.22712815X-RAY DIFFRACTION99
2.4264-2.49780.23741290.22852835X-RAY DIFFRACTION99
2.4978-2.57850.30051330.23052820X-RAY DIFFRACTION100
2.5785-2.67060.28621530.2232830X-RAY DIFFRACTION99
2.6706-2.77750.26241580.21362789X-RAY DIFFRACTION100
2.7775-2.90390.26541620.222822X-RAY DIFFRACTION100
2.9039-3.05690.28881570.212828X-RAY DIFFRACTION100
3.0569-3.24840.25561460.20462820X-RAY DIFFRACTION100
3.2484-3.49910.22441560.19842852X-RAY DIFFRACTION100
3.4991-3.8510.20281560.1852821X-RAY DIFFRACTION100
3.851-4.40780.22311280.16292881X-RAY DIFFRACTION100
4.4078-5.55150.1761540.15362847X-RAY DIFFRACTION100
5.5515-42.89580.17481660.1642878X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2521-0.08280.20370.5534-0.2427-0.1252-0.0366-0.15790.1170.06850.0386-0.0482-0.0439-0.025200.3330.05180.05350.28940.0050.377321.98627.51124.2212
20.011-0.1497-0.05190.7428-0.0569-0.00630.0687-0.02480.0595-0.17690.03490.08050.0002-0.005900.24820.0149-0.03130.21140.04320.116220.335812.329413.5118
30.0193-0.05030.00050.1588-0.01270.00390.0858-0.0614-0.00950.00190.0464-0.01180.0485-0.02120.00020.9624-0.097-0.09690.91220.18010.61132.845620.5346-1.9366
40.17830.0212-0.08030.08490.02480.0143-0.0966-0.0191-0.20860.2921-0.19330.3437-0.0556-0.0332-00.4658-0.08320.07370.37720.07460.45910.5896-31.791926.0579
50.19240.07850.05240.29740.13330.0594-0.0742-0.00480.05030.0276-0.01090.1301-0.0319-0.015200.327-0.0353-0.02860.3152-0.01210.351212.5608-17.739417.2673
6-0.00160.0324-0.00770.0427-0.00070.02330.0205-0.1128-0.40370.0275-0.03960.08860.0222-0.114800.4479-0.080.0030.38020.0530.608418.3164-31.069429.2405
70.00030.0129-0.0449-0.01050.0213-0.0043-0.1446-0.1012-0.19540.1046-0.0641-0.009-0.1375-0.0004-00.3234-0.0386-0.03550.25730.00440.437723.1355-30.052418.8565
80.0111-0.0131-0.0413-0.01750.031-0.0893-0.0879-0.0644-0.17260.01020.0241-0.0826-0.0131-0.0195-00.25850.020.00630.2328-0.03850.358538.368-27.515116.9525
90.02380.01120.03370.0164-0.00910.006-0.01920.0761-0.0258-0.060.3481-0.1467-0.09520.048900.47310.01090.08760.3653-0.04710.323841.4995-14.58139.9485
100.0149-0.053-0.00020.0259-0.01110.00040.0762-0.0671-0.5152-0.05220.168-0.437-0.0316-0.038100.2925-0.03320.03110.234-0.11980.246831.002-19.92989.7815
110.11140.1596-0.10050.07320.05530.0216-0.0075-0.0368-0.1166-0.03650.035-0.0780.0112-0.0327-00.27460.0081-0.01340.26080.01180.170628.7133-11.784622.0143
120.07360.0770.0028-0.0118-0.01740.024-0.24480.0362-0.1462-0.15230.26060.0687-0.35010.0984-00.2284-0.0698-0.04870.2692-0.00610.23921.7763-14.257112.8585
130.19950.09590.26380.1892-0.19190.15880.1848-0.2852-0.06020.07140.0156-0.13350.0720.0853-00.25780.0547-0.0670.4494-0.11110.40660.4383-4.210637.3406
140.32920.0839-0.2640.3842-0.12390.01210.0338-0.2641-0.1421-0.0511-0.0103-0.20010.06980.013800.24940.0178-0.0560.4736-0.08580.529360.3884-6.430133.8155
150.1526-0.3134-0.12560.23280.1322-0.05140.0179-0.09430.0758-0.17750.0795-0.3032-0.0952-0.060900.2259-0.0460.08610.2412-0.05840.458556.04612.146122.0783
160.2629-0.0960.07680.18570.09490.02140.0132-0.04570.0753-0.02620.0659-0.2822-0.0016-0.02800.18640.00980.02960.2081-0.03450.216548.73140.198724.2227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:112 )A-1 - 112
2X-RAY DIFFRACTION2( CHAIN A AND RESID 113:304 )A113 - 304
3X-RAY DIFFRACTION3( CHAIN A AND RESID 305:306 )A305 - 306
4X-RAY DIFFRACTION4( CHAIN B AND RESID -1:16 )B-1 - 16
5X-RAY DIFFRACTION5( CHAIN B AND RESID 17:80 )B17 - 80
6X-RAY DIFFRACTION6( CHAIN B AND RESID 81:113 )B81 - 113
7X-RAY DIFFRACTION7( CHAIN B AND RESID 114:137 )B114 - 137
8X-RAY DIFFRACTION8( CHAIN B AND RESID 138:191 )B138 - 191
9X-RAY DIFFRACTION9( CHAIN B AND RESID 192:209 )B192 - 209
10X-RAY DIFFRACTION10( CHAIN B AND RESID 210:227 )B210 - 227
11X-RAY DIFFRACTION11( CHAIN B AND RESID 228:282 )B228 - 282
12X-RAY DIFFRACTION12( CHAIN B AND RESID 283:306 )B283 - 306
13X-RAY DIFFRACTION13( CHAIN C AND RESID -1:47 )C-1 - 47
14X-RAY DIFFRACTION14( CHAIN C AND RESID 48:113 )C48 - 113
15X-RAY DIFFRACTION15( CHAIN C AND RESID 114:209 )C114 - 209
16X-RAY DIFFRACTION16( CHAIN C AND RESID 210:304 )C210 - 304

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