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- PDB-3nyc: Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3nyc
TitleCrystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase
ComponentsD-Arginine Dehydrogenase
KeywordsOXIDOREDUCTASE / D-Arginine Dehydrogenase / FAD / Imino-Arginine
Function / homology
Function and homology information


D-arginine dehydrogenase / D-amino-acid dehydrogenase activity / arginine metabolic process / 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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-IAR / FAD-dependent catabolic D-arginine dehydrogenase DauA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.06 Å
AuthorsFu, G. / Weber, I.T.
CitationJournal: Biochemistry / Year: 2010
Title: Conformational changes and substrate recognition in Pseudomonas aeruginosa D-arginine dehydrogenase.
Authors: Fu, G. / Yuan, H. / Li, C. / Lu, C.D. / Gadda, G. / Weber, I.T.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-Arginine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3633
Polymers41,4061
Non-polymers9582
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.178, 78.082, 89.719
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 D-Arginine Dehydrogenase


Mass: 41405.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA3863, PAO1 / Plasmid: pBAD-His-6 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10
References: UniProt: Q9HXE3, Oxidoreductases; Acting on the CH-NH2 group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-IAR / (2E)-5-[(diaminomethylidene)amino]-2-iminopentanoic acid


Type: peptide linking / Mass: 172.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M 2-(N-morpholino)-ethanesulfonic acid (MES) pH 6.5-7.0, 5% glycerol, 6-10% (w/v) PEG6000. , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99999 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.06→50 Å / Num. all: 190545 / Num. obs: 190545 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.062
Reflection shellResolution: 1.06→1.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.3 / % possible all: 69.1

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Processing

Software
NameClassification
HKL-2000data collection
SGXPROmodel building
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: AB INITIO
Starting model: NONE

Resolution: 1.06→10 Å / Num. parameters: 32658 / Num. restraintsaints: 41983 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: CONJUGAGE GRADIENT MINIMIZATION
RfactorNum. reflection% reflectionSelection details
Rfree0.16 9501 5 %RANDOM
Rwork0.134 ---
obs0.135 169858 96.3 %-
all-189984 --
Refine analyzeNum. disordered residues: 32 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3425.8
Refinement stepCycle: LAST / Resolution: 1.06→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 65 460 3441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.111
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.05
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.108

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