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- PDB-9ixd: Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hyd... -

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Basic information

Entry
Database: PDB / ID: 9ixd
TitleCrystal structure of Copper-bound 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
COPPER (II) ION / COPPER (I) ION / : / N(omega)-hydroxy-L-arginine amidinohydrolase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: 8IUW
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

Downloads & links

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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)60,3198
Polymers60,0332
Non-polymers2866
Water9,044502
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 area0 Å2
ΔGint0 kcal/mol
Surface area11580 Å2
MethodPISA
2
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1684
Polymers30,0171
Non-polymers1513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-22 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.400, 47.145, 59.393
Angle α, β, γ (deg.)83.69, 84.70, 70.27
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 508 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.15 %
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: 1.35 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: 1.35 Å / Relative weight: 1
ReflectionResolution: 1.5→44.22 Å / Num. obs: 70228 / % possible obs: 93.3 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Χ2: 1.04 / Net I/σ(I): 13.7 / Num. measured all: 256067
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 87 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.704 / Num. measured all: 11971 / Num. unique obs: 3255 / CC1/2: 0.708 / Rpim(I) all: 0.426 / Rrim(I) all: 0.824 / Χ2: 0.75 / Net I/σ(I) obs: 1.9

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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: 1.5→44.22 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2046 3450 4.91 %
Rwork0.1682 --
obs0.1699 70216 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 6 502 4592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064298
X-RAY DIFFRACTIONf_angle_d0.8535888
X-RAY DIFFRACTIONf_dihedral_angle_d15.268618
X-RAY DIFFRACTIONf_chiral_restr0.056676
X-RAY DIFFRACTIONf_plane_restr0.006792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.33711490.28622458X-RAY DIFFRACTION87
1.52-1.540.29421270.2432524X-RAY DIFFRACTION88
1.54-1.570.23141240.22492615X-RAY DIFFRACTION90
1.57-1.590.25221280.20522560X-RAY DIFFRACTION90
1.59-1.620.22051310.19172627X-RAY DIFFRACTION91
1.62-1.640.2441320.18782596X-RAY DIFFRACTION91
1.64-1.670.22231470.18582631X-RAY DIFFRACTION92
1.67-1.710.23631390.18832644X-RAY DIFFRACTION92
1.71-1.740.26361320.18912672X-RAY DIFFRACTION92
1.74-1.780.22491380.19022632X-RAY DIFFRACTION93
1.78-1.820.21251430.17972647X-RAY DIFFRACTION93
1.82-1.870.20841430.17762632X-RAY DIFFRACTION93
1.87-1.920.25031280.17742706X-RAY DIFFRACTION93
1.92-1.970.20921490.17982664X-RAY DIFFRACTION93
1.97-2.040.23071400.17442680X-RAY DIFFRACTION94
2.04-2.110.23271370.17252695X-RAY DIFFRACTION94
2.11-2.190.18251550.16652657X-RAY DIFFRACTION94
2.19-2.290.21591420.16522680X-RAY DIFFRACTION94
2.29-2.410.18651420.1762737X-RAY DIFFRACTION95
2.41-2.560.22611520.16872758X-RAY DIFFRACTION96
2.56-2.760.21941270.16942755X-RAY DIFFRACTION96
2.76-3.040.22981490.17342742X-RAY DIFFRACTION97
3.04-3.480.18521280.15822814X-RAY DIFFRACTION97
3.48-4.380.15511300.13842817X-RAY DIFFRACTION98
4.39-44.220.17291380.15272823X-RAY DIFFRACTION98

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