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- PDB-4myf: Crystal structure of Trypanosoma cruzi formiminoglutamase(oxidize... -

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Basic information

Entry
Database: PDB / ID: 4myf
TitleCrystal structure of Trypanosoma cruzi formiminoglutamase(oxidized) with Mn2+2 at pH 6.0
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 / 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 1.2Sep 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.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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7473
Polymers34,6371
Non-polymers1102
Water3,207178
1
A: Formiminoglutamase
hetero molecules

A: Formiminoglutamase
hetero molecules

A: Formiminoglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2419
Polymers103,9123
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 area6080 Å2
ΔGint-55 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.548, 129.548, 42.665
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-642-

HOH

21A-654-

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 / 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.: 178 / 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: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: An apo-T.cruzi fromiminoglutamase(ox) crystal was soaked in 20 mM MnCl2, 0.1 M sodium malonate (pH 6.0), 25% PEG 3350 for 12 hours, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 17, 2012 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 24348 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 9.978
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.273 / Rsym value: 0.466 / % possible all: 97.3

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Processing

Software
NameVersionClassification
CrystalCleardata 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→25.14 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 1207 5.11 %random
Rwork0.1706 ---
obs0.1726 23603 95.18 %-
all-24341 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.915 Å2 / ksol: 0.336 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3175 Å20 Å20 Å2
2---0.3175 Å2-0 Å2
3---0.6349 Å2
Refinement stepCycle: LAST / Resolution: 1.799→25.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 2 178 2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072289
X-RAY DIFFRACTIONf_angle_d13095
X-RAY DIFFRACTIONf_dihedral_angle_d15.259829
X-RAY DIFFRACTIONf_chiral_restr0.074331
X-RAY DIFFRACTIONf_plane_restr0.004414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7991-1.87110.25611250.21732323X-RAY DIFFRACTION88
1.8711-1.95630.24221180.19492388X-RAY DIFFRACTION91
1.9563-2.05930.24271380.18642439X-RAY DIFFRACTION94
2.0593-2.18830.2381230.17812484X-RAY DIFFRACTION95
2.1883-2.35720.23111450.16822520X-RAY DIFFRACTION96
2.3572-2.59410.20611360.17022539X-RAY DIFFRACTION98
2.5941-2.9690.211520.17852547X-RAY DIFFRACTION98
2.969-3.73870.21651430.1682544X-RAY DIFFRACTION98
3.7387-25.14290.16131270.14752612X-RAY DIFFRACTION99

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