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- PDB-6lug: Crystal structure of N(omega)-hydroxy-L-arginine hydrolase -

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Basic information

Entry
Database: PDB / ID: 6lug
TitleCrystal 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 / SAD / MAD / Resolution: 1.9 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 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)60,2536
Polymers60,0332
Non-polymers2204
Water7,710428
1
A: 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 area110 Å2
ΔGint-5 kcal/mol
Surface area11610 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 area110 Å2
ΔGint-4 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.440, 47.020, 59.350
Angle α, β, γ (deg.)83.440, 84.590, 70.310
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
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: 1.8924 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8924 Å / Relative weight: 1
ReflectionResolution: 1.9→44.1 Å / Num. obs: 35027 / % possible obs: 95.3 % / Redundancy: 12.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.03 / Rrim(I) all: 0.11 / Net I/σ(I): 19 / Num. measured all: 434720 / Scaling rejects: 614
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.288 / Num. unique obs: 1975 / CC1/2: 0.942 / Rpim(I) all: 0.131 / Rrim(I) all: 0.318 / % possible all: 79.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
XDS20190315data reduction
XSCALE20190315data scaling
SHARP2.8phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.9→44.1 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 1768 5.05 %RANDOM
Rwork0.2035 33226 --
obs0.2059 34994 95.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.84 Å2 / Biso mean: 19.9904 Å2 / Biso min: 6.8 Å2
Refinement stepCycle: final / Resolution: 1.9→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 4 428 4482
Biso mean--22.29 26.26 -
Num. residues----544
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.31191060.21682168227480
1.95-2.010.30371360.22512341247787
2.01-2.080.32161370.222475261294
2.08-2.150.2931430.20562581272495
2.15-2.240.30451530.18862566271996
2.24-2.340.25941280.18472590271896
2.34-2.460.26751290.19162628275797
2.46-2.620.23911360.19662592272898
2.62-2.820.24061230.20172661278498
2.82-3.10.26941090.20372681279098
3.1-3.550.21681510.20082645279699
3.55-4.470.23121390.193226772816100
4.47-44.10.22561780.22572621279999

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