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- PDB-7euk: Crystal structure of N(omega)-hydroxy-L-arginine hydrolase in com... -

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Basic information

Entry
Database: PDB / ID: 7euk
TitleCrystal structure of N(omega)-hydroxy-L-arginine hydrolase in complex with L-Orn
ComponentsN(omega)-hydroxy-L-arginine amidinohydrolase
KeywordsANTIBIOTIC / hydrolase
Function / homology
Function and homology information


Nomega-hydroxy-L-arginine amidinohydrolase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / L-ornithine / N(omega)-hydroxy-L-arginine amidinohydrolase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOda, K. / Matoba, Y.
CitationJournal: Protein Sci. / Year: 2022
Title: Catalytic mechanism of DcsB: Arginase framework used for hydrolyzing its inhibitor.
Authors: Oda, K. / Sakaguchi, T. / Matoba, Y.
History
DepositionMay 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N(omega)-hydroxy-L-arginine amidinohydrolase
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4108
Polymers60,0332
Non-polymers3766
Water11,403633
1
A: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1514
Polymers30,0171
Non-polymers1343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area11620 Å2
MethodPISA
2
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2594
Polymers30,0171
Non-polymers2423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.392, 46.963, 59.317
Angle α, β, γ (deg.)83.530, 84.710, 70.140
Int Tables number1
Space group name H-MP1

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Components

#1: Protein N(omega)-hydroxy-L-arginine amidinohydrolase / hydroxyarginase


Mass: 30016.701 Da / Num. of mol.: 2 / Fragment: N(omega)-hydroxy-L-arginine amidinohydrolase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: dcsB / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D2Z025, Nomega-hydroxy-L-arginine amidinohydrolase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.76 % / Mosaicity: 0.21 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: PEG 4000, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→44 Å / Num. obs: 88405 / % possible obs: 96 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.6 / Num. measured all: 652069 / Scaling rejects: 6333
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.4-1.426.10.4032704044280.8933.893.5
7.54-445.70.0433405910.99855.799.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LUH

6luh


Resolution: 1.4→44 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 16.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1791 4419 5.01 %
Rwork0.158 83872 -
obs0.1591 88291 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.18 Å2 / Biso mean: 16.4895 Å2 / Biso min: 5.06 Å2
Refinement stepCycle: final / Resolution: 1.4→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 14 633 4697
Biso mean--19.81 25.85 -
Num. residues----544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.420.24971880.21462718290694
1.42-1.430.21071470.19592652279993
1.43-1.450.21441730.18822756292994
1.45-1.470.21011460.18752722286894
1.47-1.490.21191530.18852747290094
1.49-1.510.19881330.17732718285194
1.51-1.530.22831330.18512753288693
1.53-1.550.18471300.17362752288294
1.55-1.580.17591420.16012752289494
1.58-1.60.16481390.15842756289595
1.6-1.630.18061330.15172770290395
1.63-1.660.17031590.15132786294595
1.66-1.690.15091380.15912768290695
1.69-1.730.19981390.16132815295496
1.73-1.760.19461590.16722753291296
1.76-1.80.19181620.1642786294896
1.8-1.850.19331610.15892823298496
1.85-1.90.17881370.15882782291996
1.9-1.960.17781590.15922816297596
1.96-2.020.16181550.16152800295597
2.02-2.090.19241570.15872805296297
2.09-2.180.16081340.15562833296797
2.18-2.270.16321290.15242856298597
2.27-2.390.17751350.15612874300998
2.39-2.540.19011250.16152881300698
2.54-2.740.18351490.16172857300698
2.74-3.020.18431480.16022864301298
3.02-3.450.17991670.15052859302699
3.45-4.350.17051250.13432921304699
4.35-440.15221640.15412897306199

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