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- PDB-6pbm: Pseudopaline Dehydrogenase with NADP+ bound -

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Basic information

Entry
Database: PDB / ID: 6pbm
TitlePseudopaline Dehydrogenase with NADP+ bound
ComponentsPseudopaline Dehydrogenase
Keywordsoxidoreductase / biosynthetic protein / Opine Metallophore Dehydrogenase Enzyme
Function / homologyOxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / NAD(P)-binding domain superfamily / plasma membrane / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pseudopaline synthase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMcFarlane, J.S. / Lamb, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM127655-01 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores.
Authors: McFarlane, J.S. / Zhang, J. / Wang, S. / Lei, X. / Moran, G.R. / Lamb, A.L.
History
DepositionJun 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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: Pseudopaline Dehydrogenase
B: Pseudopaline Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,20213
Polymers99,1572
Non-polymers2,04511
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint5 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.854, 53.865, 96.881
Angle α, β, γ (deg.)90.00, 99.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-847-

HOH

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Components

#1: Protein Pseudopaline Dehydrogenase


Mass: 49578.500 Da / Num. of mol.: 2
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: PA4835 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HUX5, Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.45
Details: 100 mM BisTris pH 5.45, 200 mM ammonium acetate, and 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→39.64 Å / Num. obs: 126498 / % possible obs: 98.1 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 1.57→1.6 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 5877 / CC1/2: 0.724

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C4N

6c4n


Resolution: 1.57→39.64 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.44
RfactorNum. reflection% reflection
Rfree0.1818 2000 1.58 %
Rwork0.1649 --
obs0.1652 126478 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.57→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6603 0 132 542 7277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016921
X-RAY DIFFRACTIONf_angle_d1.1779423
X-RAY DIFFRACTIONf_dihedral_angle_d10.9865632
X-RAY DIFFRACTIONf_chiral_restr0.0571033
X-RAY DIFFRACTIONf_plane_restr0.0071227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5688-1.6080.26831370.23638488X-RAY DIFFRACTION94
1.608-1.65150.25791420.21498895X-RAY DIFFRACTION99
1.6515-1.70010.23071430.20468895X-RAY DIFFRACTION99
1.7001-1.7550.22721430.19358889X-RAY DIFFRACTION98
1.755-1.81770.19481420.18088872X-RAY DIFFRACTION98
1.8177-1.89050.19461400.1758634X-RAY DIFFRACTION96
1.8905-1.97650.19961430.17178944X-RAY DIFFRACTION99
1.9765-2.08070.19111440.16428950X-RAY DIFFRACTION99
2.0807-2.21110.17591440.15778978X-RAY DIFFRACTION99
2.2111-2.38180.19361400.15218764X-RAY DIFFRACTION97
2.3818-2.62140.18321450.15718999X-RAY DIFFRACTION99
2.6214-3.00060.18171460.16059061X-RAY DIFFRACTION99
3.0006-3.780.18161430.16198895X-RAY DIFFRACTION97
3.78-39.65410.1421480.15369214X-RAY DIFFRACTION98

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