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- PDB-6s4d: Crystal Structure of the Homospermidine Synthase (HSS) variant W2... -

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Basic information

Entry
Database: PDB / ID: 6s4d
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant W229F 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: 1.8 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
DepositionJun 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,9277
Polymers105,9972
Non-polymers1,9315
Water14,988832
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-17 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.110, 110.009, 158.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Homospermidine synthase / HSS


Mass: 52998.457 Da / Num. of mol.: 2 / Mutation: W229F, G1 to 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-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H11NO3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
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: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.57→90.312 Å / Num. obs: 134527 / % possible obs: 91.6 % / Redundancy: 6.8 % / Rrim(I) all: 0.325 / Net I/σ(I): 4.4
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 1408

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLP

4plp


Resolution: 1.8→90.312 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.2079 4933 5.1 %
Rwork0.1733 --
obs0.1751 96772 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→90.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7408 0 127 832 8367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017880
X-RAY DIFFRACTIONf_angle_d0.84710774
X-RAY DIFFRACTIONf_dihedral_angle_d19.5972869
X-RAY DIFFRACTIONf_chiral_restr0.0511155
X-RAY DIFFRACTIONf_plane_restr0.0051418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.36611640.33972983X-RAY DIFFRACTION97
1.8205-1.84190.31321380.32392945X-RAY DIFFRACTION98
1.8419-1.86430.34361550.31263001X-RAY DIFFRACTION98
1.8643-1.88790.34251630.30183023X-RAY DIFFRACTION98
1.8879-1.91280.34031500.29252996X-RAY DIFFRACTION98
1.9128-1.9390.30261560.28733057X-RAY DIFFRACTION98
1.939-1.96670.31461660.27512963X-RAY DIFFRACTION98
1.9667-1.99610.27731590.26643004X-RAY DIFFRACTION98
1.9961-2.02720.26261710.24892990X-RAY DIFFRACTION98
2.0272-2.06050.28571670.23833020X-RAY DIFFRACTION99
2.0605-2.0960.25481470.21773058X-RAY DIFFRACTION99
2.096-2.13410.22921650.21073030X-RAY DIFFRACTION99
2.1341-2.17520.26291600.20253018X-RAY DIFFRACTION99
2.1752-2.21960.23621800.19163059X-RAY DIFFRACTION99
2.2196-2.26790.20771740.18113019X-RAY DIFFRACTION99
2.2679-2.32060.22861630.1763093X-RAY DIFFRACTION99
2.3206-2.37870.21331380.17473051X-RAY DIFFRACTION99
2.3787-2.4430.21521730.16343036X-RAY DIFFRACTION99
2.443-2.51490.20471710.16243088X-RAY DIFFRACTION99
2.5149-2.5960.19451580.16363055X-RAY DIFFRACTION100
2.596-2.68880.22251840.16483051X-RAY DIFFRACTION99
2.6888-2.79650.21921870.16473060X-RAY DIFFRACTION100
2.7965-2.92380.18841690.15653065X-RAY DIFFRACTION98
2.9238-3.07790.19931390.16243115X-RAY DIFFRACTION100
3.0779-3.27080.20051820.16373094X-RAY DIFFRACTION100
3.2708-3.52330.15571650.14553139X-RAY DIFFRACTION100
3.5233-3.87790.18211930.14033101X-RAY DIFFRACTION100
3.8779-4.4390.1661570.12533171X-RAY DIFFRACTION100
4.439-5.59260.16221640.12773207X-RAY DIFFRACTION100
5.5926-90.42550.18121750.17333347X-RAY DIFFRACTION99

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