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- PDB-6s6g: Crystal Structure of the Homospermidine Synthase (HSS) variant E1... -

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Basic information

Entry
Database: PDB / ID: 6s6g
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant E117Q from Blastochloris viridis in Complex with NAD
ComponentsHomospermidine synthase
KeywordsTRANSFERASE / Homospermidine Synthase / Rossmann Fold / NAD / Putrescine
Function / homology
Function and homology information


homospermidine synthase (spermidine-specific) activity / homospermidine synthase / homospermidine synthase activity
Similarity search - Function
homospermidine synthase like / Homospermidine synthase-like, C-terminal / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich ...homospermidine synthase like / Homospermidine synthase-like, C-terminal / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHelfrich, F. / Scheidig, A.J.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural and catalytic characterization of Blastochloris viridis and Pseudomonas aeruginosa homospermidine synthases supports the essential role of cation-pi interaction.
Authors: Helfrich, F. / Scheidig, A.J.
History
DepositionJul 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 20, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / database_2 / pdbx_data_processing_status / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homospermidine synthase
B: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7937
Polymers106,0732
Non-polymers1,7205
Water15,799877
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-52 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.340, 110.551, 158.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Homospermidine synthase / HSS


Mass: 53036.508 Da / Num. of mol.: 2 / Mutation: E117Q, G1 -G4 expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastochloris viridis (bacteria) / Gene: hss / Production host: Escherichia coli (E. coli) / References: UniProt: O32323, homospermidine synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium acetate, Ammonium acetate, PEG 10000, NDSB-201, Agmatine sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→79.22 Å / Num. obs: 134938 / % possible obs: 96.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 21.33 Å2 / Rrim(I) all: 0.133 / Net I/σ(I): 7.1
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 3613

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLP

4plp


Resolution: 1.6→60.3829 Å / SU ML: 0.2093 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5844
RfactorNum. reflection% reflection
Rfree0.197 6713 4.98 %
Rwork0.1695 --
obs0.1709 134783 96.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.71 Å2
Refinement stepCycle: LAST / Resolution: 1.6→60.3829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7298 0 111 877 8286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00537804
X-RAY DIFFRACTIONf_angle_d0.94610681
X-RAY DIFFRACTIONf_chiral_restr0.05181156
X-RAY DIFFRACTIONf_plane_restr0.00521382
X-RAY DIFFRACTIONf_dihedral_angle_d21.66622841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.4789850.41191819X-RAY DIFFRACTION41.19
1.62-1.640.3682140.34923450X-RAY DIFFRACTION79.39
1.64-1.660.32831990.31774053X-RAY DIFFRACTION92.45
1.66-1.680.30092290.29544263X-RAY DIFFRACTION96.58
1.68-1.70.30142150.27654281X-RAY DIFFRACTION97.8
1.7-1.720.30242110.26944354X-RAY DIFFRACTION98.34
1.72-1.750.282200.25154296X-RAY DIFFRACTION98.37
1.75-1.780.26082460.23524355X-RAY DIFFRACTION98.54
1.78-1.80.24952150.22174293X-RAY DIFFRACTION98.56
1.8-1.830.24482360.22034317X-RAY DIFFRACTION98.66
1.83-1.860.23732030.2134385X-RAY DIFFRACTION98.65
1.86-1.90.24512180.20934351X-RAY DIFFRACTION98.55
1.9-1.930.24552520.20344322X-RAY DIFFRACTION98.71
1.93-1.970.23652270.1974338X-RAY DIFFRACTION98.72
1.97-2.020.22572190.18864394X-RAY DIFFRACTION99.14
2.02-2.060.21432220.18824364X-RAY DIFFRACTION99.2
2.06-2.120.21232290.18384370X-RAY DIFFRACTION99.18
2.12-2.170.19942180.16314417X-RAY DIFFRACTION99.02
2.17-2.240.18672360.15734373X-RAY DIFFRACTION99.52
2.24-2.310.19112310.1514393X-RAY DIFFRACTION99.14
2.31-2.390.18192640.14984360X-RAY DIFFRACTION99.57
2.39-2.490.1712280.14724420X-RAY DIFFRACTION99.34
2.49-2.60.18222210.14984424X-RAY DIFFRACTION99.17
2.6-2.740.20342180.16174480X-RAY DIFFRACTION99.66
2.74-2.910.1712300.15514427X-RAY DIFFRACTION99.66
2.91-3.130.18422370.16044461X-RAY DIFFRACTION99.77
3.13-3.450.18852500.15884477X-RAY DIFFRACTION99.89
3.45-3.950.19742460.14434520X-RAY DIFFRACTION99.98
3.95-4.970.12972360.12584567X-RAY DIFFRACTION99.92
4.97-60.38290.1832580.16834746X-RAY DIFFRACTION99.72

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