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- PDB-7eul: Crystal structure of C86H-H196S mutant of N(omega)-hydroxy-L-argi... -

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Basic information

Entry
Database: PDB / ID: 7eul
TitleCrystal structure of C86H-H196S mutant of N(omega)-hydroxy-L-arginine hydrolase
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 / : / arginase activity / antibiotic biosynthetic process / manganese ion binding / cytosol
Similarity search - Function
Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / N(omega)-hydroxy-L-arginine amidinohydrolase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2146
Polymers30,0011
Non-polymers2135
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-18 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.499, 50.343, 52.941
Angle α, β, γ (deg.)90.000, 99.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30000.639 Da / Num. of mol.: 1 / Fragment: N(omega)-hydroxy-L-arginine amidinohydrolase / Mutation: C86H, H196S
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.: 3 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 1.86 Å3/Da / Density % sol: 33.95 % / Mosaicity: 0.24 °
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: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→41.93 Å / Num. obs: 39175 / % possible obs: 99.9 % / Redundancy: 4.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Rrim(I) all: 0.07 / Net I/σ(I): 13 / Num. measured all: 181105 / Scaling rejects: 72
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
1.45-1.474.70.381907119320.9080.1950.433.199.8
7.94-41.934.30.05211472670.9890.0280.0625.299.4

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Processing

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

6luh


Resolution: 1.45→41.93 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 1959 5 %
Rwork0.169 37195 -
obs0.1702 39154 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.6 Å2 / Biso mean: 21.608 Å2 / Biso min: 8.71 Å2
Refinement stepCycle: final / Resolution: 1.45→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 5 250 2266
Biso mean--17.65 30.92 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.490.21991520.21126372789100
1.49-1.530.22621510.19326302781100
1.53-1.570.23261390.186926432782100
1.57-1.620.1961500.175126352785100
1.62-1.680.21641350.17852630276599
1.68-1.750.23041250.17426472772100
1.75-1.830.21141380.177726752813100
1.83-1.920.17731220.170826422764100
1.92-2.040.23411230.174126602783100
2.04-2.20.21231540.171726562810100
2.2-2.420.1731370.159626622799100
2.42-2.770.20311410.174826732814100
2.77-3.490.18891320.166926972829100
3.49-41.930.17021600.156827082868100

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