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- PDB-9ixf: Crystal structure of Manganese-free N(omega)-hydroxy-L-arginine h... -

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Basic information

Entry
Database: PDB / ID: 9ixf
TitleCrystal structure of Manganese-free N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86.
ComponentsN(omega)-hydroxy-L-arginine amidinohydrolase
KeywordsHYDROLASE
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: 1.75 Å
AuthorsOda, K. / Matoba, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2024
Title: Copper inactivates DcsB by oxidizing the metal ligand Cys86 to sulfinic acid.
Authors: Oda, K. / Komaguchi, K. / Matoba, Y.
History
DepositionJul 27, 2024Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 20, 2024ID: 8IUV
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed
Revision 1.2Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)60,1867
Polymers60,0332
Non-polymers1525
Water8,125451
1
A: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0963
Polymers30,0171
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-8 kcal/mol
Surface area11590 Å2
MethodPISA
2
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0904
Polymers30,0171
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-20 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.876, 46.683, 58.222
Angle α, β, γ (deg.)85.39, 86.78, 70.54
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.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.96 %
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: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→43.92 Å / Num. obs: 44308 / % possible obs: 96.8 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.048 / Rrim(I) all: 0.092 / Χ2: 0.91 / Net I/σ(I): 9.8 / Num. measured all: 158923
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 95.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.351 / Num. measured all: 8413 / Num. unique obs: 2372 / CC1/2: 0.884 / Rpim(I) all: 0.217 / Rrim(I) all: 0.413 / Χ2: 0.57 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→43.92 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 2175 4.91 %
Rwork0.158 --
obs0.16 44301 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 5 451 4532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074158
X-RAY DIFFRACTIONf_angle_d0.8855689
X-RAY DIFFRACTIONf_dihedral_angle_d13.376592
X-RAY DIFFRACTIONf_chiral_restr0.06658
X-RAY DIFFRACTIONf_plane_restr0.006761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.26831380.22573X-RAY DIFFRACTION95
1.79-1.830.20971430.18112612X-RAY DIFFRACTION96
1.83-1.880.23441560.16832576X-RAY DIFFRACTION96
1.88-1.930.22161580.1642590X-RAY DIFFRACTION96
1.93-1.980.21250.15932627X-RAY DIFFRACTION96
1.98-2.050.1761410.15972615X-RAY DIFFRACTION96
2.05-2.120.20241370.15882608X-RAY DIFFRACTION96
2.12-2.20.20761300.16192590X-RAY DIFFRACTION96
2.2-2.310.24211130.15912665X-RAY DIFFRACTION96
2.31-2.430.19931370.16262635X-RAY DIFFRACTION96
2.43-2.580.19661250.16472645X-RAY DIFFRACTION98
2.58-2.780.2066880.16612728X-RAY DIFFRACTION98
2.78-3.060.21971560.17282647X-RAY DIFFRACTION98
3.06-3.50.19111450.15712674X-RAY DIFFRACTION98
3.5-4.410.19871590.13212643X-RAY DIFFRACTION98
4.41-43.920.16771240.15272698X-RAY DIFFRACTION98

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