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- PDB-4myl: Crystal structure of Trypanosoma cruzi Formiminoglutamase (oxidiz... -

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Basic information

Entry
Database: PDB / ID: 4myl
TitleCrystal structure of Trypanosoma cruzi Formiminoglutamase (oxidized) at pH 4.6
ComponentsFormiminoglutamase
KeywordsHYDROLASE / arginase/deacetylase (a/b) fold
Function / homology
Function and homology information


putrescine biosynthetic process from arginine, via agmatine / 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: 1.531 Å
AuthorsHai, Y. / Dugery, R.J. / Healy, D. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2013
Title: Formiminoglutamase from trypanosoma cruzi is an arginase-like manganese metalloenzyme.
Authors: Hai, Y. / Dugery, R.J. / Healy, D. / Christianson, D.W.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formiminoglutamase


Theoretical massNumber of molelcules
Total (without water)34,6371
Polymers34,6371
Non-polymers00
Water2,882160
1
A: Formiminoglutamase

A: Formiminoglutamase

A: Formiminoglutamase


Theoretical massNumber of molelcules
Total (without water)103,9123
Polymers103,9123
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 area5200 Å2
ΔGint-19 kcal/mol
Surface area29680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.437, 129.437, 42.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-420-

HOH

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Components

#1: Protein Formiminoglutamase


Mass: 34637.227 Da / Num. of mol.: 1 / Mutation: S302P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pET vector / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4DSA0, formimidoylglutamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: A 4 UL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 UM MnCl2] was mixed with a 4 UL drop of precipitant solution [25% PEG 3350, 0.1 M sodium acetate (pH 4.6)] on a ...Details: A 4 UL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 UM MnCl2] was mixed with a 4 UL drop of precipitant solution [25% PEG 3350, 0.1 M sodium acetate (pH 4.6)] on a siliconized cover slide and equilibrated against a 500 UL reservoir of precipitant solution, VAPOR DIFFUSION, HANGING 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 27, 2012
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: 0.282
ReflectionResolution: 1.53→50 Å / Num. obs: 40029 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 24.071
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 2.224 / Rsym value: 0.534 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASER(CCP4)phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2a0m

2a0m


Resolution: 1.531→37.365 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.14 / Phase error: 22.86 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1612 1994 5.11 %random
Rwork0.1343 ---
obs0.1357 39028 97.39 %-
all-40029 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.545 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso mean: 18.448 Å2
Baniso -1Baniso -2Baniso -3
1--1.8042 Å20 Å20 Å2
2---1.8042 Å2-0 Å2
3---3.6084 Å2
Refinement stepCycle: LAST / Resolution: 1.531→37.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 0 160 2372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082287
X-RAY DIFFRACTIONf_angle_d1.0433095
X-RAY DIFFRACTIONf_dihedral_angle_d15.545832
X-RAY DIFFRACTIONf_chiral_restr0.074331
X-RAY DIFFRACTIONf_plane_restr0.005415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.532-1.57030.25491370.22582437X-RAY DIFFRACTION86
1.5703-1.61270.23541210.21812526X-RAY DIFFRACTION88
1.6127-1.66020.2151440.20582548X-RAY DIFFRACTION89
1.6602-1.71380.21741420.18882567X-RAY DIFFRACTION91
1.7138-1.7750.21161480.18012655X-RAY DIFFRACTION92
1.775-1.84610.20391290.16632675X-RAY DIFFRACTION93
1.8461-1.93010.18611530.15982640X-RAY DIFFRACTION94
1.9301-2.03190.19091470.15362698X-RAY DIFFRACTION94
2.0319-2.15910.17771580.14452697X-RAY DIFFRACTION94
2.1591-2.32580.14251430.13972687X-RAY DIFFRACTION95
2.3258-2.55980.16491390.13192730X-RAY DIFFRACTION95
2.5598-2.930.17161310.12872735X-RAY DIFFRACTION95
2.93-3.69080.1251450.10152688X-RAY DIFFRACTION95
3.6908-33.90810.1171250.09482706X-RAY DIFFRACTION95

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