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- PDB-7lol: The structure of Agmatinase from E. Coli at 1.8 A displaying urea... -

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Basic information

Entry
Database: PDB / ID: 7lol
TitleThe structure of Agmatinase from E. Coli at 1.8 A displaying urea and agmatine
ComponentsAgmatinase
KeywordsHYDROLASE
Function / homology
Function and homology information


agmatinase / agmatinase activity / putrescine biosynthetic process from arginine / spermidine biosynthetic process / manganese ion binding
Similarity search - Function
Agmatinase / Agmatinase-related / Ureohydrolase, manganese-binding site / Arginase family signature. / Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
AGMATINE / : / UREA / Agmatinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMaturana, P. / Figueroa, M. / Gonzalez-Ordenes, F. / Villalobos, P. / Martinez-Oyanedel, J. / Uribe, E.A. / Castro-Fernandez, V.
Funding support Chile, 3items
OrganizationGrant numberCountry
Comision Nacional Cientifica y Technologica (CONICYT)FONDECYT 11181133 Chile
Comision Nacional Cientifica y Technologica (CONICYT)REDI170497 Chile
Comision Nacional Cientifica y Technologica (CONICYT)Fondequip EQM140151 Chile
CitationJournal: Int J Mol Sci / Year: 2021
Title: Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity.
Authors: Maturana, P. / Orellana, M.S. / Herrera, S.M. / Martinez, I. / Figueroa, M. / Martinez-Oyanedel, J. / Castro-Fernandez, V. / Uribe, E.
History
DepositionFeb 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agmatinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0717
Polymers33,5941
Non-polymers4776
Water2,684149
1
A: Agmatinase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)204,42742
Polymers201,5646
Non-polymers2,86336
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_434x-y-2/3,-y-4/3,-z-1/31
crystal symmetry operation18_444-x-2/3,-x+y-1/3,-z-1/31
Buried area27910 Å2
ΔGint-162 kcal/mol
Surface area49840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.746, 81.746, 207.436
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-404-

MN

21A-406-

TRS

31A-406-

TRS

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Agmatinase / Agmatine ureohydrolase / AUH


Mass: 33593.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: speB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A4S5B4F2, agmatinase

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Non-polymers , 5 types, 155 molecules

#2: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 38.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Agmatinase at 12 mg/mL in Buffer 25 mM Tris-HCl pH 8.0, 2 mM MnCl2. Condition: 0.1 M phosphate/citrate pH 4.2 and 40% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→35.79 Å / Num. obs: 25154 / % possible obs: 99.87 % / Redundancy: 19.9 % / Biso Wilson estimate: 27.14 Å2 / Rmerge(I) obs: 0.06576 / Rrim(I) all: 0.06753 / Net I/σ(I): 28.76
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 3.61 / Num. unique obs: 2475 / Rrim(I) all: 0.9161

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.14_3260refinement
Aimlessdata scaling
BALBESphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NPI

3npi


Resolution: 1.8→35.79 Å / SU ML: 0.1271 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6338 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1947 1244 4.95 %
Rwork0.1701 23883 -
obs0.1713 25127 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 24 149 2429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01452330
X-RAY DIFFRACTIONf_angle_d1.35363160
X-RAY DIFFRACTIONf_chiral_restr0.091348
X-RAY DIFFRACTIONf_plane_restr0.007416
X-RAY DIFFRACTIONf_dihedral_angle_d16.9009833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.26431400.23542609X-RAY DIFFRACTION99.89
1.87-1.960.23991480.20362615X-RAY DIFFRACTION99.96
1.96-2.060.25831390.18152599X-RAY DIFFRACTION99.96
2.06-2.190.22351160.17672649X-RAY DIFFRACTION99.86
2.19-2.360.23161480.16882642X-RAY DIFFRACTION100
2.36-2.60.20861530.1762617X-RAY DIFFRACTION99.93
2.6-2.970.19171330.18072670X-RAY DIFFRACTION99.96
2.97-3.740.19271050.16992720X-RAY DIFFRACTION99.96
3.74-50.16191620.15332762X-RAY DIFFRACTION99.49

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