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- PDB-7rdf: Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 7rdf
TitleCrystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F co-crystallized in the presence of D-arginine
ComponentsFAD-dependent catabolic D-arginine dehydrogenase DauA
KeywordsFLAVOPROTEIN / Flavin versatility / Flavin N5 adduct / 6-OH-FAD / D-arginine Dehydrogenase / ligand identity
Function / homology
Function and homology information


D-arginine dehydrogenase / D-amino-acid dehydrogenase activity / arginine metabolic process / L-arginine catabolic process / nucleotide binding / cytoplasm
Similarity search - Function
FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-4R2 / 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / FAD-dependent catabolic D-arginine dehydrogenase DauA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsReis, R.A.G. / Iyer, A. / Agniswamy, A. / Weber, I.T. / Gadda, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1506518 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase.
Authors: Iyer, A. / Reis, R.A.G. / Agniswamy, J. / Weber, I.T. / Gadda, G.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: FAD-dependent catabolic D-arginine dehydrogenase DauA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6917
Polymers40,5951
Non-polymers2,0976
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.010, 76.330, 76.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FAD-dependent catabolic D-arginine dehydrogenase DauA / D-arginine dehydrogenase / DADH / D-arginine utilization protein A / Dau


Mass: 40594.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: dauA, PA3863 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXE3, D-arginine dehydrogenase

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Non-polymers , 5 types, 408 molecules

#2: Chemical ChemComp-4R2 / [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(~{E})-4-carbamimidamidobut-2-enoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate


Mass: 912.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N12O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-6FA / 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE


Mass: 801.549 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O16P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.2 % / Description: Green-colored pyramidal crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 13% (w/v) PEG 3350, 6% (w/v) PEG 6000, 20 mM TRIS-Cl, pH 7.0, 10% glycerol, 5 mM D-arginine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.29→47.28 Å / Num. obs: 86350 / % possible obs: 97.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 11.94 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.03159 / Rsym value: 0.086 / Net I/σ(I): 16.35
Reflection shellResolution: 1.29→1.36 Å / Rmerge(I) obs: 0.1497 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 11210 / CC1/2: 0.906 / Rsym value: 0.0357

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NYE

3nye


Resolution: 1.29→40.19 Å / SU ML: 0.0926 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.3488
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1565 4206 4.87 %
Rwork0.1262 82074 -
obs0.1278 86280 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.77 Å2
Refinement stepCycle: LAST / Resolution: 1.29→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 141 402 3400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053516
X-RAY DIFFRACTIONf_angle_d0.91034865
X-RAY DIFFRACTIONf_chiral_restr0.083500
X-RAY DIFFRACTIONf_plane_restr0.0101655
X-RAY DIFFRACTIONf_dihedral_angle_d23.8062569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.310.1855810.16842188X-RAY DIFFRACTION78.73
1.31-1.320.20241040.14522360X-RAY DIFFRACTION84.1
1.32-1.340.16591060.13172491X-RAY DIFFRACTION89.27
1.34-1.360.14211470.11912641X-RAY DIFFRACTION95.54
1.36-1.380.15241480.12132666X-RAY DIFFRACTION96.6
1.38-1.390.15361070.11742774X-RAY DIFFRACTION97.99
1.39-1.410.17251320.11772733X-RAY DIFFRACTION99.03
1.41-1.430.16991400.12182741X-RAY DIFFRACTION98.97
1.43-1.460.14921510.11572731X-RAY DIFFRACTION98.7
1.46-1.480.16371530.10782743X-RAY DIFFRACTION98.74
1.48-1.510.13261200.10362767X-RAY DIFFRACTION98.94
1.51-1.530.15981570.10322743X-RAY DIFFRACTION99.18
1.53-1.560.13631430.09662768X-RAY DIFFRACTION99.32
1.56-1.60.12891330.09772779X-RAY DIFFRACTION99.35
1.6-1.630.13841490.10362760X-RAY DIFFRACTION99.39
1.63-1.670.1411490.10972768X-RAY DIFFRACTION99.29
1.67-1.710.15971380.10882774X-RAY DIFFRACTION99.52
1.71-1.760.13861500.10832758X-RAY DIFFRACTION99.66
1.76-1.810.13741700.11282762X-RAY DIFFRACTION99.76
1.81-1.870.15621460.11682813X-RAY DIFFRACTION99.76
1.87-1.930.14561440.11732784X-RAY DIFFRACTION99.69
1.93-2.010.14081320.11932814X-RAY DIFFRACTION99.93
2.01-2.10.13621410.12512794X-RAY DIFFRACTION99.86
2.1-2.210.15191360.12732858X-RAY DIFFRACTION100
2.21-2.350.14981550.13292789X-RAY DIFFRACTION99.97
2.35-2.530.16191390.13582835X-RAY DIFFRACTION100
2.53-2.790.18081420.1412868X-RAY DIFFRACTION100
2.79-3.190.15621670.14032834X-RAY DIFFRACTION99.97
3.19-4.020.16051770.12382861X-RAY DIFFRACTION99.41
4.02-40.190.1791490.14592877X-RAY DIFFRACTION95.46

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