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- PDB-9ixc: Crystal structure of Manganese-rebound N(omega)-hydroxy-L-arginin... -

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Basic information

Entry
Database: PDB / ID: 9ixc
TitleCrystal structure of Manganese-rebound 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: 1.26 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: 8IUU
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)60,2777
Polymers60,0332
Non-polymers2445
Water10,485582
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 area250 Å2
ΔGint-12 kcal/mol
Surface area11590 Å2
MethodPISA
2
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1273
Polymers30,0171
Non-polymers1102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-15 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.940, 46.743, 58.338
Angle α, β, γ (deg.)85.33, 86.91, 70.59
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 1.96 Å3/Da / Density % sol: 37.27 %
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: 1.26→43.99 Å / Num. obs: 110843 / % possible obs: 89.9 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.047 / Rrim(I) all: 0.073 / Χ2: 0.58 / Net I/σ(I): 6.1 / Num. measured all: 225171
Reflection shellResolution: 1.26→1.28 Å / % possible obs: 49.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.548 / Num. measured all: 5911 / Num. unique obs: 3037 / CC1/2: 0.538 / Rpim(I) all: 0.485 / Rrim(I) all: 0.734 / Χ2: 0.59 / 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: 1.26→35.22 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1862 5468 4.93 %
Rwork0.1648 --
obs0.1658 110835 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.26→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 5 582 4644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054183
X-RAY DIFFRACTIONf_angle_d0.8635729
X-RAY DIFFRACTIONf_dihedral_angle_d16.727602
X-RAY DIFFRACTIONf_chiral_restr0.082661
X-RAY DIFFRACTIONf_plane_restr0.006768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.270.2492860.24341901X-RAY DIFFRACTION48
1.27-1.290.26751070.22342053X-RAY DIFFRACTION54
1.29-1.310.2671150.22172436X-RAY DIFFRACTION61
1.31-1.320.19951270.21472731X-RAY DIFFRACTION71
1.32-1.340.23181880.21773434X-RAY DIFFRACTION87
1.34-1.360.21691620.21153508X-RAY DIFFRACTION89
1.36-1.380.2121960.19893555X-RAY DIFFRACTION91
1.38-1.40.22781470.19243640X-RAY DIFFRACTION93
1.4-1.420.21282140.18833675X-RAY DIFFRACTION94
1.42-1.440.19122040.18353612X-RAY DIFFRACTION94
1.44-1.470.21762070.18313690X-RAY DIFFRACTION94
1.47-1.490.21691720.1763672X-RAY DIFFRACTION94
1.49-1.520.20062200.1713688X-RAY DIFFRACTION94
1.52-1.550.19832000.17133657X-RAY DIFFRACTION95
1.55-1.590.18261950.16393689X-RAY DIFFRACTION94
1.59-1.620.18492270.16283686X-RAY DIFFRACTION95
1.62-1.670.17911800.16183749X-RAY DIFFRACTION95
1.67-1.710.19951950.16613687X-RAY DIFFRACTION95
1.71-1.760.19971720.17063727X-RAY DIFFRACTION95
1.76-1.820.18642120.16673700X-RAY DIFFRACTION96
1.82-1.880.20421870.15913751X-RAY DIFFRACTION96
1.88-1.960.18232110.16443756X-RAY DIFFRACTION96
1.96-2.050.19331940.15993745X-RAY DIFFRACTION96
2.05-2.150.17891700.15883773X-RAY DIFFRACTION96
2.15-2.290.19241620.15583793X-RAY DIFFRACTION96
2.29-2.470.18072120.1623752X-RAY DIFFRACTION97
2.47-2.710.18822250.16943793X-RAY DIFFRACTION98
2.71-3.110.18782060.1693837X-RAY DIFFRACTION98
3.11-3.910.16892020.14553828X-RAY DIFFRACTION98
3.91-35.220.14911730.14923849X-RAY DIFFRACTION98

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