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- PDB-7lba: E. coli Agmatinase -

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Basic information

Entry
Database: PDB / ID: 7lba
TitleE. coli Agmatinase
ComponentsAgmatinase
KeywordsHYDROLASE / Agmatine Polyamine amidinohydrolase ureohydrolase metallohydrolase
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChitrakar, I. / Ahmed, S.F. / Torelli, A.T. / French, J.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1750637 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR029205 United States
CitationJournal: Plos One / Year: 2021
Title: Structure of the E. coli agmatinase, SPEB.
Authors: Chitrakar, I. / Ahmed, S.F. / Torelli, A.T. / French, J.B.
History
DepositionJan 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agmatinase
B: Agmatinase
C: Agmatinase
D: Agmatinase
E: Agmatinase
F: Agmatinase
G: Agmatinase
H: Agmatinase
I: Agmatinase
J: Agmatinase
K: Agmatinase
L: Agmatinase
M: Agmatinase
N: Agmatinase
O: Agmatinase
P: Agmatinase
Q: Agmatinase
R: Agmatinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)654,46745
Polymers652,98318
Non-polymers1,48327
Water22,5011249
1
A: Agmatinase
B: Agmatinase
C: Agmatinase
D: Agmatinase
E: Agmatinase
F: Agmatinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,32018
Polymers217,6616
Non-polymers65912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26380 Å2
ΔGint-241 kcal/mol
Surface area47840 Å2
MethodPISA
2
G: Agmatinase
H: Agmatinase
I: Agmatinase
J: Agmatinase
K: Agmatinase
L: Agmatinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,32018
Polymers217,6616
Non-polymers65912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26520 Å2
ΔGint-242 kcal/mol
Surface area48030 Å2
MethodPISA
3
M: Agmatinase
N: Agmatinase
O: Agmatinase
P: Agmatinase
Q: Agmatinase
R: Agmatinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,8269
Polymers217,6616
Non-polymers1653
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25530 Å2
ΔGint-190 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.809, 139.809, 222.987
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Agmatinase / Agmatine ureohydrolase / AUH


Mass: 36276.859 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: speB, WG5_03731 / Production host: Escherichia coli (E. coli) / References: UniProt: S0XV43, agmatinase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.98 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 3.5 M Sodium Formate, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.418
11K, H, -L20.087
11-h,-k,l30.403
11-K, -H, -L40.092
ReflectionResolution: 2.2→82.02 Å / Num. obs: 247407 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.056 / Rrim(I) all: 0.136 / Net I/σ(I): 11.2 / Num. measured all: 1435676 / Scaling rejects: 254
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.245.90.61173154123090.7850.2730.673.4100
12.05-82.026.20.043934615120.9990.0190.04722.199.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZ4

4dz4


Resolution: 2.2→82.02 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.139 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 12405 5 %RANDOM
Rwork0.1795 ---
obs0.1812 234929 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.77 Å2 / Biso mean: 27.061 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.94 Å20 Å20 Å2
2--2.94 Å20 Å2
3----5.89 Å2
Refinement stepCycle: final / Resolution: 2.2→82.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42271 0 27 1249 43547
Biso mean--45.81 19.67 -
Num. residues----5481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01343252
X-RAY DIFFRACTIONr_bond_other_d0.0010.01739204
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.63458716
X-RAY DIFFRACTIONr_angle_other_deg1.0761.57790681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36555463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92522.5842318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.501156789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.55515252
X-RAY DIFFRACTIONr_chiral_restr0.0380.25562
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0249484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.029348
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 908 -
Rwork0.244 17419 -
all-18327 -
obs--99.74 %

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