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- PDB-6p9d: Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 6p9d
TitleCrystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F variant with FAD - Yellow fraction
ComponentsFAD-dependent catabolic D-arginine dehydrogenase DauA
KeywordsFLAVOPROTEIN / Oxidoreductase / Dehydrogenase Pseudomonas aeruginosa 6-OH-FAD D-amino acids
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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / FAD-dependent catabolic D-arginine dehydrogenase DauA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.329 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 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 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)41,7516
Polymers40,5951
Non-polymers1,1565
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.100, 74.030, 77.190
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M Tris-Cl pH 7.0-7.3, 10% glycerol, and 12-13% (w/v) PEG 3350, 5-10% PEG 6000
PH range: 7.0-7.3

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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: 1.329→39.95 Å / Num. obs: 79369 / % possible obs: 99.37 % / Redundancy: 2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.01957 / Net I/σ(I): 17.19
Reflection shellResolution: 1.329→1.377 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 7650 / CC1/2: 0.882 / % possible all: 96.96

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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: 1.329→37.01 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 4120 5.19 %0.1621
Rwork0.1313 ---
obs0.1329 79364 99.37 %-
Refinement stepCycle: LAST / Resolution: 1.329→37.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 0 77 358 3291
LS refinement shellResolution: 1.329→1.3446 Å /
RfactorNum. reflection
Rfree0.2007 131
Rwork0.1778 -

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