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- PDB-7eun: Crystal structure of N(omega)-hydroxy-L-arginine hydrolase in com... -

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Basic information

Entry
Database: PDB / ID: 7eun
TitleCrystal structure of N(omega)-hydroxy-L-arginine hydrolase in complex with ABH
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
2(S)-AMINO-6-BORONOHEXANOIC ACID / : / N(omega)-hydroxy-L-arginine amidinohydrolase
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsOda, K. / Matoba, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
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)60,51810
Polymers60,0332
Non-polymers4858
Water10,701594
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 area11810 Å2
MethodPISA
2
B: N(omega)-hydroxy-L-arginine amidinohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3676
Polymers30,0171
Non-polymers3505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.577, 47.208, 59.641
Angle α, β, γ (deg.)83.540, 84.440, 70.200
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.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ABH / 2(S)-AMINO-6-BORONOHEXANOIC ACID


Mass: 191.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15BNO5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.01 Å3/Da / Density % sol: 38.76 % / Mosaicity: 0.1 °
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: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.28→44.26 Å / Num. obs: 116740 / % possible obs: 95.5 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Net I/σ(I): 10.9 / Num. measured all: 428211 / Scaling rejects: 239
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
1.28-1.33.70.3522112256770.9060.2140.4134.293.6
7.01-44.263.60.06726327250.9770.0420.07918.197.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 6LUH

6luh


Resolution: 1.28→44.26 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 12.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1383 5806 4.98 %RANDOM
Rwork0.1149 110872 --
obs0.1161 116678 95.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.07 Å2 / Biso mean: 16.5292 Å2 / Biso min: 5.02 Å2
Refinement stepCycle: final / Resolution: 1.28→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4058 0 35 594 4687
Biso mean--13.74 30.17 -
Num. residues----545
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.28-1.290.17591980.14493631382993
1.29-1.310.16681790.13243618379793
1.31-1.330.14372020.12523585378793
1.33-1.340.1512070.11973619382694
1.34-1.360.1732110.11673589380094
1.36-1.380.15511890.1133639382894
1.38-1.40.12171840.10643624380894
1.4-1.420.13761830.10293691387494
1.42-1.440.12641800.09883601378194
1.44-1.470.12251930.09683639383294
1.47-1.490.11662080.09463616382494
1.49-1.520.13171670.09583637380494
1.52-1.550.11861840.0973679386394
1.55-1.580.10792210.09173585380695
1.58-1.610.12491960.09443721391795
1.61-1.650.10672140.09083680389496
1.65-1.690.13221930.09623722391596
1.69-1.740.12162200.0993699391996
1.74-1.790.13931680.10083764393296
1.79-1.850.12891510.10273752390396
1.85-1.910.1411890.10773727391697
1.91-1.990.14161750.10963808398397
1.99-2.080.12812170.1093720393797
2.08-2.190.14391800.11153777395797
2.19-2.330.12761790.1113811399097
2.33-2.510.13422100.11483747395798
2.51-2.760.15231900.12713800399098
2.76-3.160.15431990.13013803400298
3.16-3.980.13252030.12163807401098
3.98-44.260.15652160.14093781399798

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