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- PDB-6pld: Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 6pld
TitleCrystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F variant with 6-OH-FAD - Green fraction
ComponentsFAD-dependent catabolic D-arginine dehydrogenase DauA
KeywordsFLAVOPROTEIN / Flavin / 6-OH-FAD
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 / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
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: 1.55 Å
AuthorsReis, R.A.G. / Iyer, A. / Agniswamy, J. / Gannavaram, S. / Weber, I. / Gadda, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1506518 United States
CitationJournal: Biochemistry / Year: 2021
Title: A Single-Point Mutation in d-Arginine Dehydrogenase Unlocks a Transient Conformational State Resulting in Altered Cofactor Reactivity.
Authors: Iyer, A. / Reis, R.A.G. / Gannavaram, S. / Momin, M. / Spring-Connell, A.M. / Orozco-Gonzalez, Y. / Agniswamy, J. / Hamelberg, D. / Weber, I.T. / Gozem, S. / Wang, S. / Germann, M.W. / Gadda, G.
History
DepositionJun 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,0559
Polymers40,5951
Non-polymers1,4608
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.780, 73.910, 76.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 / Mutation: Y249F
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
#2: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.09 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.05 M Tris-Cl pH 6.5-7.0, 10% glycerol, and 12-13% (w/v) PEG 3350, 5-10% PEG 5000
PH range: 6.5-7.0

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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: Feb 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→59.78 Å / Num. obs: 48055 / % possible obs: 96.1 % / Redundancy: 7 % / Biso Wilson estimate: 12.484 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2284 / CC1/2: 0.896 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NYE

3nye


Resolution: 1.55→39.789 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.58
RfactorNum. reflection% reflection
Rfree0.2027 2416 5.03 %
Rwork0.1632 --
obs0.1652 48002 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→39.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2853 0 97 364 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063304
X-RAY DIFFRACTIONf_angle_d1.1794555
X-RAY DIFFRACTIONf_dihedral_angle_d9.7152606
X-RAY DIFFRACTIONf_chiral_restr0.054480
X-RAY DIFFRACTIONf_plane_restr0.006606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.58160.23361250.18972593X-RAY DIFFRACTION93
1.5816-1.6160.23641560.18372576X-RAY DIFFRACTION93
1.616-1.65360.22691440.18362588X-RAY DIFFRACTION94
1.6536-1.6950.2341470.17772565X-RAY DIFFRACTION94
1.695-1.74080.19621480.1692598X-RAY DIFFRACTION94
1.7408-1.7920.23841320.16732642X-RAY DIFFRACTION94
1.792-1.84990.22281340.1712653X-RAY DIFFRACTION95
1.8499-1.9160.20531440.17092650X-RAY DIFFRACTION96
1.916-1.99270.17691350.15722673X-RAY DIFFRACTION96
1.9927-2.08340.191430.15162680X-RAY DIFFRACTION96
2.0834-2.19320.17411850.15772663X-RAY DIFFRACTION97
2.1932-2.33060.20171280.15342722X-RAY DIFFRACTION97
2.3306-2.51060.19481280.16422747X-RAY DIFFRACTION97
2.5106-2.76310.21611550.16392712X-RAY DIFFRACTION97
2.7631-3.16280.20091250.16032812X-RAY DIFFRACTION98
3.1628-3.98430.18461330.14632818X-RAY DIFFRACTION98
3.9843-39.80240.21151540.17392894X-RAY DIFFRACTION96

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