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- PDB-6luh: High resolution structure of N(omega)-hydroxy-L-arginine hydrolase -

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Basic information

Entry
Database: PDB / ID: 6luh
TitleHigh resolution structure of N(omega)-hydroxy-L-arginine hydrolase
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 / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsOda, K. / Matoba, Y.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal structure of an Nomega-hydroxy-L-arginine hydrolase found in the D-cycloserine biosynthetic pathway.
Authors: Oda, K. / Shimotani, N. / Kuroda, T. / Matoba, Y.
History
DepositionJan 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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
Water11,710650
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 area110 Å2
ΔGint-8 kcal/mol
Surface area11700 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 area20 Å2
ΔGint-1 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.326, 47.057, 59.261
Angle α, β, γ (deg.)83.570, 84.630, 70.130
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: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: PEG 4000, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→44.09 Å / Num. obs: 72157 / % possible obs: 96.5 % / Redundancy: 7.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.117 / Net I/σ(I): 11.2 / Num. measured all: 519387 / Scaling rejects: 2596
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.449 / Num. unique obs: 3541 / CC1/2: 0.9 / Rpim(I) all: 0.178 / Rrim(I) all: 0.484 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
SHARP2.8phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6LUG

6lug


Resolution: 1.5→44.09 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 23.97
RfactorNum. reflection% reflection
Rfree0.2302 3549 4.93 %
Rwork0.1997 --
obs0.2012 72042 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.32 Å2 / Biso mean: 14.1934 Å2 / Biso min: 0.63 Å2
Refinement stepCycle: final / Resolution: 1.5→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 5 650 4705
Biso mean--10.22 22.39 -
Num. residues----544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.24851590.20122686284594
1.52-1.540.27341360.21762669280594
1.54-1.570.23331290.20462711284095
1.57-1.590.25691330.21052675280895
1.59-1.620.25131370.2142725286295
1.62-1.640.26481460.20042661280795
1.64-1.670.24771520.20092735288795
1.67-1.710.20471390.20692696283595
1.71-1.740.27341440.21812735287996
1.74-1.780.28661420.21822710285296
1.78-1.820.23751450.22112724286996
1.82-1.870.25191490.21352719286896
1.87-1.920.24511260.20672751287796
1.92-1.970.26261570.21292670282795
1.97-2.040.25431320.22748288095
2.04-2.110.24121370.19342765290297
2.11-2.190.20641660.18322737290397
2.19-2.290.20591550.19312746290197
2.29-2.410.22321380.19112770290897
2.41-2.560.2331500.19252816296698
2.56-2.760.22111340.20252780291498
2.76-3.040.22511460.20592754290098
3.04-3.480.19851300.19432843297398
3.48-4.380.21351280.19162828295699
4.39-44.090.21951390.192728392978100

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