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

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Basic information

Entry
Database: PDB / ID: 9ixg
TitleCrystal structure of Manganese-free N(omega)-hydroxy-L-arginine hydrolase without 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: 2.14 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: 8IUS
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)60,1616
Polymers60,0332
Non-polymers1284
Water4,612256
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-7 kcal/mol
Surface area11490 Å2
MethodPISA
2
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0653
Polymers30,0171
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-19 kcal/mol
Surface area10760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.872, 46.756, 58.139
Angle α, β, γ (deg.)84.98, 86.40, 70.57
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.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 36.92 %
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: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.14→43.98 Å / Num. obs: 24286 / % possible obs: 97 % / Redundancy: 1.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.041 / Rrim(I) all: 0.058 / Χ2: 0.23 / Net I/σ(I): 5.3 / Num. measured all: 44917
Reflection shellResolution: 2.14→2.2 Å / % possible obs: 96 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.105 / Num. measured all: 3828 / Num. unique obs: 2000 / CC1/2: 0.966 / Rpim(I) all: 0.105 / Rrim(I) all: 0.149 / Χ2: 0.17 / Net I/σ(I) obs: 2

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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: 2.14→35.25 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1200 4.94 %
Rwork0.1585 --
obs0.1616 24276 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.14→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 4 256 4329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094150
X-RAY DIFFRACTIONf_angle_d0.9185677
X-RAY DIFFRACTIONf_dihedral_angle_d12.086588
X-RAY DIFFRACTIONf_chiral_restr0.056657
X-RAY DIFFRACTIONf_plane_restr0.006759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.230.23341180.15782620X-RAY DIFFRACTION96
2.23-2.330.22561400.15972513X-RAY DIFFRACTION96
2.33-2.450.25871250.16772549X-RAY DIFFRACTION96
2.45-2.60.23861300.17172537X-RAY DIFFRACTION96
2.6-2.80.23441360.17772546X-RAY DIFFRACTION97
2.8-3.090.26341240.17722557X-RAY DIFFRACTION97
3.09-3.530.23581310.16032611X-RAY DIFFRACTION98
3.53-4.450.19561570.14052569X-RAY DIFFRACTION98
4.45-35.250.19691390.15012574X-RAY DIFFRACTION98

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