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- PDB-2a0m: Arginase superfamily protein from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 2a0m
TitleArginase superfamily protein from Trypanosoma cruzi
ComponentsARGINASE SUPERFAMILY PROTEIN
KeywordsHYDROLASE / STRUCTURAL GENOMICS / ARGINASE / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homology
Function and homology information


putrescine biosynthetic process from arginine, using agmatinase / agmatinase 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 cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.603 Å
AuthorsArakaki, T.L. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Methods Mol.Biol. / Year: 2008
Title: Structural genomics of pathogenic protozoa: an overview.
Authors: Fan, E. / Baker, D. / Fields, S. / Gelb, M.H. / Buckner, F.S. / Van Voorhis, W.C. / Phizicky, E. / Dumont, M. / Mehlin, C. / Grayhack, E. / Sullivan, M. / Verlinde, C. / Detitta, G. / ...Authors: Fan, E. / Baker, D. / Fields, S. / Gelb, M.H. / Buckner, F.S. / Van Voorhis, W.C. / Phizicky, E. / Dumont, M. / Mehlin, C. / Grayhack, E. / Sullivan, M. / Verlinde, C. / Detitta, G. / Meldrum, D.R. / Merritt, E.A. / Earnest, T. / Soltis, M. / Zucker, F. / Myler, P.J. / Schoenfeld, L. / Kim, D. / Worthey, L. / Lacount, D. / Vignali, M. / Li, J. / Mondal, S. / Massey, A. / Carroll, B. / Gulde, S. / Luft, J. / Desoto, L. / Holl, M. / Caruthers, J. / Bosch, J. / Robien, M. / Arakaki, T. / Holmes, M. / Le Trong, I. / Hol, W.G.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 16, 2013Group: Database references
Revision 1.4Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.
Remark 999SEQUENCE The sequence of this protein can be found at GeneDB with id TC00.1047053507963.20.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARGINASE SUPERFAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7142
Polymers34,6781
Non-polymers351
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ARGINASE SUPERFAMILY PROTEIN
hetero molecules

A: ARGINASE SUPERFAMILY PROTEIN
hetero molecules

A: ARGINASE SUPERFAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1416
Polymers104,0353
Non-polymers1063
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 area6030 Å2
ΔGint-54 kcal/mol
Surface area30210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.875, 128.875, 42.671
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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Components

#1: Protein ARGINASE SUPERFAMILY PROTEIN


Mass: 34678.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053507963.20 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q4DSA0, formimidoylglutamase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.97 Å3/Da / Density % sol: 37.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.4 ul protein 8.7 mg/ml, 0.4 ul crystallization buffer, 100mM potassium bromide, 42% PEG 1000, 100mM Na citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 32939 / % possible obs: 94.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.952
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID
1.6-1.6657.20.5370.99720101
1.66-1.7289.40.5051.52830981
1.72-1.899.70.422.41734851
1.8-1.91000.2834.05534591
1.9-2.021000.1925.37834721
2.02-2.171000.1218.79634791
2.17-2.391000.08512.40834991
2.39-2.741000.05817.63534571
2.74-3.451000.04224.11834971
3.45-501000.04723.58234831

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Phasing

Phasing MRRfactor: 0.365 / Cor.coef. Fo:Fc: 0.643
Highest resolutionLowest resolution
Rotation3 Å39.86 Å
Translation3 Å39.86 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0005 24/04/2001refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1.6data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: low resolution SAD structure

Resolution: 1.603→39.873 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.167 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 1646 4.997 %random
Rwork0.168 ---
obs-32939 94.928 %-
Solvent computationSolvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.897 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.603→39.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2286 0 1 202 2489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222348
X-RAY DIFFRACTIONr_bond_other_d0.0010.022108
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.9573177
X-RAY DIFFRACTIONr_angle_other_deg0.83334895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60423.423111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.74815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5481518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02512
X-RAY DIFFRACTIONr_nbd_refined0.2190.2489
X-RAY DIFFRACTIONr_nbd_other0.1860.22051
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21165
X-RAY DIFFRACTIONr_nbtor_other0.0810.21180
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.210
X-RAY DIFFRACTIONr_mcbond_it1.2211.51914
X-RAY DIFFRACTIONr_mcbond_other0.2261.5614
X-RAY DIFFRACTIONr_mcangle_it1.37522368
X-RAY DIFFRACTIONr_mcangle_other0.63222063
X-RAY DIFFRACTIONr_scbond_it2.443999
X-RAY DIFFRACTIONr_scbond_other0.78431837
X-RAY DIFFRACTIONr_scangle_it3.2084.5806
X-RAY DIFFRACTIONr_scangle_other1.2494.52832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.603-1.6450.334710.2751367261255.054
1.645-1.690.3351100.271863245580.367
1.69-1.7390.2681160.232225244095.943
1.739-1.7920.2291160.2122228234999.787
1.792-1.8510.2471180.18822002318100
1.851-1.9160.2541040.17721022206100
1.916-1.9880.1971000.17720392139100
1.988-2.0690.157960.16519162012100
2.069-2.160.198930.16419092002100
2.16-2.2650.179990.15917901889100
2.265-2.3880.205880.15616931781100
2.388-2.5320.19920.16316131705100
2.532-2.7060.195740.16215151589100
2.706-2.9220.177820.16513891471100
2.922-3.1990.18640.16312991363100
3.199-3.5730.185700.15611751245100
3.573-4.1210.165640.1410151079100
4.121-5.0330.139370.139884921100
5.033-7.0620.231360.191684720100
7.062-39.8730.237160.175387403100

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