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- PDB-7lox: The structure of Agmatinase from E. Coli at 3.2 A displaying guan... -

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Basic information

Entry
Database: PDB / ID: 7lox
TitleThe structure of Agmatinase from E. Coli at 3.2 A displaying guanidine in the active site
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
GUANIDINE / : / Agmatinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 11, 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 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Agmatinase
B: Agmatinase
C: Agmatinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,34813
Polymers100,7823
Non-polymers56610
Water00
1
A: Agmatinase
B: Agmatinase
C: Agmatinase
hetero molecules

A: Agmatinase
B: Agmatinase
C: Agmatinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,69626
Polymers201,5646
Non-polymers1,13220
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area17680 Å2
ΔGint-176 kcal/mol
Surface area54210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.028, 129.028, 88.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAASPASP(chain 'A' and (resid 16 through 26 or (resid 27...AA16 - 4316 - 43
12GLYGLYLYSLYS(chain 'A' and (resid 16 through 26 or (resid 27...AA51 - 30351 - 303
21ALAALAASPASP(chain 'B' and (resid 16 through 30 or (resid 31...BB16 - 4316 - 43
22GLYGLYLYSLYS(chain 'B' and (resid 16 through 30 or (resid 31...BB51 - 30351 - 303
31ALAALAASPASP(chain 'C' and (resid 16 through 30 or (resid 31...CC16 - 4316 - 43
32GLYGLYLYSLYS(chain 'C' and (resid 16 through 30 or (resid 31...CC51 - 30351 - 303

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Components

#1: Protein Agmatinase / Agmatine ureohydrolase / AUH


Mass: 33593.988 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: speB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4S5B4F2, agmatinase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein at 12 mg/mL in Buffer 25 mM Tris-HCl pH 8.0, 2 mM MnCl. Crystallization: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.771 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: 1.771 Å / Relative weight: 1
ReflectionResolution: 3.2→64.51 Å / Num. obs: 14314 / % possible obs: 99.87 % / Redundancy: 39.4 % / Biso Wilson estimate: 84.61 Å2 / Rmerge(I) obs: 0.1561 / Rrim(I) all: 0.1582 / Net I/σ(I): 26.7
Reflection shellResolution: 3.2→3.314 Å / Rmerge(I) obs: 0.1561 / Num. unique obs: 1418 / Rrim(I) all: 0.1582 / % possible all: 100

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Processing

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

3npi


Resolution: 3.2→64.51 Å / SU ML: 0.292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8165 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 1254 4.63 %
Rwork0.1719 25846 -
obs0.1741 27100 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.5 Å2
Refinement stepCycle: LAST / Resolution: 3.2→64.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6517 0 22 0 6539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01176680
X-RAY DIFFRACTIONf_angle_d1.39979070
X-RAY DIFFRACTIONf_chiral_restr0.07951006
X-RAY DIFFRACTIONf_plane_restr0.00951198
X-RAY DIFFRACTIONf_dihedral_angle_d17.85072355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.330.281220.22552882X-RAY DIFFRACTION100
3.33-3.480.23051290.18892899X-RAY DIFFRACTION99.97
3.48-3.660.20341620.1692860X-RAY DIFFRACTION100
3.66-3.890.1944960.17092895X-RAY DIFFRACTION100
3.89-4.190.23451420.16622876X-RAY DIFFRACTION100
4.19-4.610.24331950.16492837X-RAY DIFFRACTION99.97
4.61-5.280.17111020.15292872X-RAY DIFFRACTION100
5.28-6.650.22191500.20542888X-RAY DIFFRACTION99.93
6.65-64.510.20561560.15792837X-RAY DIFFRACTION99.04

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