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- PDB-7euq: Crystal structure of C86H-Y124N-G126H-H196S mutant of N(omega)-hy... -

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Basic information

Entry
Database: PDB / ID: 7euq
TitleCrystal structure of C86H-Y124N-G126H-H196S mutant of N(omega)-hydroxy-L-arginine hydrolase
ComponentsN(omega)-hydroxy-L-arginine amidinohydrolase
KeywordsANTIBIOTIC / hydrolase
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: 1.8 Å
AuthorsOda, K. / Matoba, Y.
CitationJournal: Protein Sci. / Year: 2022
Title: Catalytic mechanism of DcsB: Arginase framework used for hydrolyzing its inhibitor.
Authors: Oda, K. / Sakaguchi, T. / Matoba, Y.
History
DepositionMay 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)60,38210
Polymers60,0652
Non-polymers3178
Water4,396244
1
A: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2156
Polymers30,0331
Non-polymers1835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area10930 Å2
MethodPISA
2
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1674
Polymers30,0331
Non-polymers1343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area10910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.491, 49.755, 60.515
Angle α, β, γ (deg.)89.970, 72.200, 89.910
Int Tables number1
Space group name H-MP1

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Components

#1: Protein N(omega)-hydroxy-L-arginine amidinohydrolase / hydroxyarginase


Mass: 30032.662 Da / Num. of mol.: 2 / Fragment: N(omega)-hydroxy-L-arginine amidinohydrolase / Mutation: C86H, Y124N, G126H, H196S
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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.35 % / Mosaicity: 0.45 °
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: Oct 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→40.46 Å / Num. obs: 42444 / % possible obs: 96.9 % / Redundancy: 3.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.061 / Rrim(I) all: 0.114 / Net I/σ(I): 6.6 / Num. measured all: 137451 / Scaling rejects: 188
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.843.10.664776525430.8250.440.7992.396.1
9-40.463.50.05311813360.9950.0320.06211.996.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EUL

7eul


Resolution: 1.8→39.26 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.091 / SU ML: 0.118 / SU R Cruickshank DPI: 0.1456 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 2207 5.2 %RANDOM
Rwork0.1812 ---
obs0.1828 40210 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.74 Å2 / Biso mean: 26.268 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å2-0.22 Å22.36 Å2
2---0.74 Å2-0.45 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.8→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 8 244 4288
Biso mean--24.46 33.65 -
Num. residues----542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134149
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173876
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6325681
X-RAY DIFFRACTIONr_angle_other_deg1.3851.5728951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6635547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89922.13216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64815624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7891533
X-RAY DIFFRACTIONr_chiral_restr0.0750.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02826
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 139 -
Rwork0.302 3042 -
all-3181 -
obs--95.96 %

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