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- PDB-4myn: Crystal structure of Trypanosoma cruzi formiminoglutamase N114H v... -

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Basic information

Entry
Database: PDB / ID: 4myn
TitleCrystal structure of Trypanosoma cruzi formiminoglutamase N114H variant with Mn2+2
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
: / Arginase, putative
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 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 1.2Apr 2, 2014Group: Source and taxonomy
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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

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Assembly

Deposited unit
A: Formiminoglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7713
Polymers34,6611
Non-polymers1102
Water1,67593
1
A: Formiminoglutamase
hetero molecules

A: Formiminoglutamase
hetero molecules

A: Formiminoglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3139
Polymers103,9843
Non-polymers3306
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 area6350 Å2
ΔGint-55 kcal/mol
Surface area29730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.431, 129.431, 42.522
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-549-

HOH

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Components

#1: Protein Formiminoglutamase


Mass: 34661.270 Da / Num. of mol.: 1 / Mutation: N114H, 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: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Apo-enzyme was crystallized in the following conditions: 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 ...Details: Apo-enzyme was crystallized in the following conditions: 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. To obtain the Mn2+ bound form, apo-crystal was soaked in 10 mM MnCl2, 0.1 M sodium malonate (pH 7.5), 27% PEG 3350 for 24 hours, 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: Oct 19, 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
ReflectionResolution: 1.8→50 Å / Num. obs: 24658 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 18.949
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.966 / Rsym value: 0.754 / % possible all: 100

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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: 1.799→30.012 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.18 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1211 5.08 %random
Rwork0.1879 ---
obs0.1897 23858 96.66 %-
all-24658 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.837 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.9186 Å20 Å20 Å2
2---1.9186 Å2-0 Å2
3---3.8372 Å2
Refinement stepCycle: LAST / Resolution: 1.799→30.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 2 93 2380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072342
X-RAY DIFFRACTIONf_angle_d1.0253166
X-RAY DIFFRACTIONf_dihedral_angle_d15.352846
X-RAY DIFFRACTIONf_chiral_restr0.076339
X-RAY DIFFRACTIONf_plane_restr0.006423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7986-1.87060.28251170.24652294X-RAY DIFFRACTION88
1.8706-1.95570.30071310.22882417X-RAY DIFFRACTION93
1.9557-2.05880.23381410.2132471X-RAY DIFFRACTION95
2.0588-2.18780.28551300.21022535X-RAY DIFFRACTION97
2.1878-2.35660.2671210.20432588X-RAY DIFFRACTION98
2.3566-2.59370.2291520.19692553X-RAY DIFFRACTION99
2.5937-2.96870.2281410.20342584X-RAY DIFFRACTION100
2.9687-3.73910.23031470.19042596X-RAY DIFFRACTION100
3.7391-30.01650.17511310.15852609X-RAY DIFFRACTION100

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