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- PDB-8deb: Bacteroides fragilis carboxyspermidine dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 8deb
TitleBacteroides fragilis carboxyspermidine dehydrogenase
ComponentsCarboxyspermidine dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / spermidine / norspermidine / dehydrogenase / polyamine / carboxyspermidine / carboxynorspermidine
Function / homologySaccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / oxidoreductase activity / NAD(P)-binding domain superfamily / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Saccharopine dehydrogenase
Function and homology information
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMcFarlane, J.S. / Bouchey, S. / Dodd, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RL5GM118990 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Kinetic and structural characterization of carboxyspermidine dehydrogenase of polyamine biosynthesis.
Authors: Lee, D.F. / Atencio, N. / Bouchey, S. / Shoemaker, M.R. / Dodd, J.S. / Satre, M. / Miller, K.A. / McFarlane, J.S.
History
DepositionJun 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxyspermidine dehydrogenase
B: Carboxyspermidine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7344
Polymers90,2472
Non-polymers1,4872
Water7,819434
1
A: Carboxyspermidine dehydrogenase
hetero molecules

B: Carboxyspermidine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7344
Polymers90,2472
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4740 Å2
ΔGint-21 kcal/mol
Surface area29190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.228, 85.807, 98.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Carboxyspermidine dehydrogenase


Mass: 45123.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: HMPREF1080_01141 / Production host: Escherichia coli (E. coli) / References: UniProt: I9VY56
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.53 Å3/Da / Density % sol: 51.36 % / Description: Plate arrays
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.17 M ammonium acetate, 0.085 M sodium citrate, HCl, pH 5.6, 25.5% (w/v) PEG 4000, and 15% (v/v) glycerol and 0.05 M ammonium chloride

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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 PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→39.88 Å / Num. obs: 67320 / % possible obs: 99.24 % / Redundancy: 13.3 % / Biso Wilson estimate: 23.05 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.054 / Net I/σ(I): 10.4
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4147 / CC1/2: 0.623 / Rpim(I) all: 0.421 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RL6

4rl6


Resolution: 1.94→39.88 Å / SU ML: 0.1911 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2636
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 1997 2.97 %
Rwork0.1786 65307 -
obs0.1795 67304 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.76 Å2
Refinement stepCycle: LAST / Resolution: 1.94→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 96 434 6718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336443
X-RAY DIFFRACTIONf_angle_d0.63358760
X-RAY DIFFRACTIONf_chiral_restr0.0443931
X-RAY DIFFRACTIONf_plane_restr0.00391180
X-RAY DIFFRACTIONf_dihedral_angle_d14.62852394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.28461300.24364259X-RAY DIFFRACTION92.21
1.99-2.050.27321430.21844652X-RAY DIFFRACTION99.92
2.05-2.110.24621410.22844603X-RAY DIFFRACTION99.41
2.11-2.180.22461420.19534657X-RAY DIFFRACTION99.94
2.18-2.250.221420.19644630X-RAY DIFFRACTION99.71
2.25-2.340.25491420.18054645X-RAY DIFFRACTION99.81
2.34-2.450.21411440.17694680X-RAY DIFFRACTION99.88
2.45-2.580.23911420.17434641X-RAY DIFFRACTION99.87
2.58-2.740.21511420.18434677X-RAY DIFFRACTION99.67
2.74-2.950.23591430.18634688X-RAY DIFFRACTION99.92
2.95-3.250.17721450.18034716X-RAY DIFFRACTION99.96
3.25-3.720.18841450.16774731X-RAY DIFFRACTION99.71
3.72-4.680.17371470.14654779X-RAY DIFFRACTION99.9
4.69-39.880.20051490.17574949X-RAY DIFFRACTION99.65
Refinement TLS params.Method: refined / Origin x: 60.8874708617 Å / Origin y: 42.2657400647 Å / Origin z: 49.7096334372 Å
111213212223313233
T0.147205866861 Å2-0.0215306057195 Å2-0.0120878976949 Å2-0.163511309665 Å20.00857618881262 Å2--0.150640131723 Å2
L0.202951466681 °2-0.127708365551 °20.0237543331105 °2-0.40598713722 °2-0.0640582536462 °2--0.288816685282 °2
S-0.00995350056986 Å °-0.0304621698073 Å °-0.00199969124785 Å °0.0322513994744 Å °0.0141316180375 Å °-0.034823236751 Å °-0.0131674204439 Å °0.0128302199549 Å °-0.00448970108437 Å °
Refinement TLS groupSelection details: all

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