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- PDB-4mxr: Crystal structure of Trypanosoma cruzi formiminoglutamase with Mn2+2 -

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Basic information

Entry
Database: PDB / ID: 4mxr
TitleCrystal structure of Trypanosoma cruzi formiminoglutamase 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 / MOLECULAR REPLACEMENT / Resolution: 1.849 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 26, 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_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_auth_seq_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: Formiminoglutamase
B: Formiminoglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5867
Polymers69,2742
Non-polymers3125
Water4,774265
1
A: Formiminoglutamase
hetero molecules

A: Formiminoglutamase
hetero molecules

A: Formiminoglutamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,51812
Polymers103,9123
Non-polymers6069
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 area7160 Å2
ΔGint-57 kcal/mol
Surface area28780 Å2
MethodPISA
2
B: Formiminoglutamase
hetero molecules

B: Formiminoglutamase
hetero molecules

B: 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 area6300 Å2
ΔGint-52 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.922, 128.922, 85.377
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-619-

HOH

21B-569-

HOH

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Components

#1: Protein Formiminoglutamase


Mass: 34637.227 Da / Num. of mol.: 2 / 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: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 37.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: A 4 UL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 UM MnCl2, 1 mM TCEP] was mixed with a 4 UL drop of precipitant solution [31% PEG 300, 0.1 M sodium acetate (pH 4. ...Details: A 4 UL drop of protein solution [10 mg/mL protein, 50 mM bicine (pH 8.5), 100 UM MnCl2, 1 mM TCEP] was mixed with a 4 UL drop of precipitant solution [31% PEG 300, 0.1 M sodium acetate (pH 4.9)] on a siliconized cover slide and equilibrated against a 500 UL reservoir of precipitant solution at 294K. The yielded crystal is apo. To obtain the Mn2+2 bound form, this apo-crystal was soaked with 5 mM MnCl2 in 0.1 M sodium malonate (pH 8.0), 27% PEG 3350) for 24 hours, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 17, 2013 / 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: 1.85→50 Å / Num. obs: 44906 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 14.162
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.013 / Rsym value: 0.438 / % possible all: 98.8

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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: 1.849→21.964 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 2123 5.03 %random
Rwork0.1865 ---
obs0.1882 42190 93.23 %-
all-44906 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.001 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9726 Å20 Å20 Å2
2---1.9726 Å2-0 Å2
3---4.0766 Å2
Refinement stepCycle: LAST / Resolution: 1.849→21.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 10 265 4827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044685
X-RAY DIFFRACTIONf_angle_d0.7956334
X-RAY DIFFRACTIONf_dihedral_angle_d14.7371699
X-RAY DIFFRACTIONf_chiral_restr0.059676
X-RAY DIFFRACTIONf_plane_restr0.004848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8485-1.89150.30771330.24042428X-RAY DIFFRACTION85
1.8915-1.93880.32391200.25292426X-RAY DIFFRACTION85
1.9388-1.99110.26221400.23192624X-RAY DIFFRACTION91
1.9911-2.04970.27431250.20562551X-RAY DIFFRACTION89
2.0497-2.11580.27291270.21822633X-RAY DIFFRACTION92
2.1158-2.19140.2311330.19822698X-RAY DIFFRACTION94
2.1914-2.2790.24521270.20612635X-RAY DIFFRACTION91
2.279-2.38260.24591510.1982687X-RAY DIFFRACTION95
2.3826-2.50810.24171430.19222741X-RAY DIFFRACTION96
2.5081-2.6650.24811440.18762753X-RAY DIFFRACTION95
2.665-2.87030.25571440.1992737X-RAY DIFFRACTION97
2.8703-3.15840.23551630.19942795X-RAY DIFFRACTION97
3.1584-3.61370.21241510.17522795X-RAY DIFFRACTION98
3.6137-4.54620.15061700.14462784X-RAY DIFFRACTION98
4.5462-21.96530.16661520.1592780X-RAY DIFFRACTION97

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