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- PDB-6pbn: Pseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour -

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Basic information

Entry
Database: PDB / ID: 6pbn
TitlePseudopaline Dehydrogenase with (R)-Pseudopaline Soaked 1 hour
ComponentsPseudopaline Dehdyrogenase
KeywordsBIOSYNTHETIC PROTEIN / Opine Metallophore Dehydrogenase Enzyme
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / plasma membrane
Similarity search - Function
Opine metallophore dehydrogenase / Staphylopine dehydrogenase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / N-[(3S)-3-amino-3-carboxypropyl]-L-histidine / Pseudopaline synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMcFarlane, J.S. / Lamb, A.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM127655-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM103418 United States
American Heart AssociationPRE33960374 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM08545 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

Downloads & links

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Assembly

Deposited unit
A: Pseudopaline Dehdyrogenase
B: Pseudopaline Dehdyrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,35711
Polymers99,1572
Non-polymers2,2009
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-6 kcal/mol
Surface area33970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.023, 53.842, 96.867
Angle α, β, γ (deg.)90.00, 98.77, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-867-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Pseudopaline Dehdyrogenase


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

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Non-polymers , 5 types, 635 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-O77 / N-[(3S)-3-amino-3-carboxypropyl]-L-histidine


Mass: 256.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 626 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 260 mM ammonium formate, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→39.96 Å / Num. obs: 110062 / % possible obs: 98.5 % / Redundancy: 6.8 % / CC1/2: 0.998 / Net I/σ(I): 12.9
Reflection shellResolution: 1.65→1.68 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4833 / CC1/2: 0.727

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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: 1.65→39.96 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.77
RfactorNum. reflection% reflection
Rfree0.2103 2000 1.82 %
Rwork0.1736 --
obs0.1743 110028 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6599 0 144 626 7369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016897
X-RAY DIFFRACTIONf_angle_d1.2389393
X-RAY DIFFRACTIONf_dihedral_angle_d10.155609
X-RAY DIFFRACTIONf_chiral_restr0.0581030
X-RAY DIFFRACTIONf_plane_restr0.0081224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6472-1.68840.26191310.22957118X-RAY DIFFRACTION91
1.6884-1.7340.27311430.21497702X-RAY DIFFRACTION99
1.734-1.78510.26941440.20647774X-RAY DIFFRACTION99
1.7851-1.84270.24191420.19477666X-RAY DIFFRACTION99
1.8427-1.90850.24771410.18737621X-RAY DIFFRACTION98
1.9085-1.9850.21251440.18447747X-RAY DIFFRACTION99
1.985-2.07530.21381430.17557734X-RAY DIFFRACTION99
2.0753-2.18470.23251430.1677741X-RAY DIFFRACTION99
2.1847-2.32160.20461420.16167683X-RAY DIFFRACTION98
2.3216-2.50080.21591440.15957777X-RAY DIFFRACTION99
2.5008-2.75240.18161450.16567828X-RAY DIFFRACTION99
2.7524-3.15050.19621440.17277769X-RAY DIFFRACTION98
3.1505-3.96880.20161450.17047859X-RAY DIFFRACTION100
3.9688-39.97540.19661490.16768009X-RAY DIFFRACTION99

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