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

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Basic information

Entry
Database: PDB / ID: 6sep
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant W229E 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, C-terminal / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / 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 1.2Jan 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)107,2884
Polymers105,9612
Non-polymers1,3272
Water13,872770
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-31 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.170, 109.864, 158.190
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
Components on special symmetry positions
IDModelComponents
11A-991-

HOH

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Components

#1: Protein Homospermidine synthase / HSS


Mass: 52980.395 Da / Num. of mol.: 2 / Mutation: W229E
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
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: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.87→109.86 Å / Num. obs: 85769 / % possible obs: 98.7 % / Redundancy: 10.6 % / Biso Wilson estimate: 18.69 Å2 / Rrim(I) all: 1.23381 / Net I/σ(I): 2.1
Reflection shellResolution: 1.87→1.91 Å / Num. unique obs: 3354 / Rrim(I) all: 0.77686

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Cootmodel building
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLP

4plp


Resolution: 2.2→90.31 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.5722
RfactorNum. reflection% reflection
Rfree0.245 2595 4.84 %
Rwork0.1932 --
obs0.1957 53657 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.96 Å2
Refinement stepCycle: LAST / Resolution: 2.2→90.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7388 0 88 770 8246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00257769
X-RAY DIFFRACTIONf_angle_d0.604810621
X-RAY DIFFRACTIONf_chiral_restr0.04291149
X-RAY DIFFRACTIONf_plane_restr0.00361397
X-RAY DIFFRACTIONf_dihedral_angle_d19.82722823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.34971240.28182525X-RAY DIFFRACTION94.4
2.24-2.280.32051240.27392508X-RAY DIFFRACTION94.51
2.28-2.330.29361570.25592609X-RAY DIFFRACTION98.26
2.33-2.380.30221520.25162619X-RAY DIFFRACTION99.21
2.38-2.440.31731250.24512675X-RAY DIFFRACTION99.22
2.44-2.50.31251300.23752685X-RAY DIFFRACTION99.58
2.5-2.560.30581350.23512645X-RAY DIFFRACTION99.75
2.56-2.640.25481470.22432699X-RAY DIFFRACTION99.86
2.64-2.720.33811350.2272684X-RAY DIFFRACTION99.86
2.72-2.820.26751240.21332676X-RAY DIFFRACTION99.89
2.82-2.940.27071480.20112677X-RAY DIFFRACTION100
2.94-3.070.26031210.19432733X-RAY DIFFRACTION100
3.07-3.230.25051360.18732680X-RAY DIFFRACTION99.93
3.23-3.430.23551330.17432728X-RAY DIFFRACTION99.97
3.43-3.70.21661490.14822715X-RAY DIFFRACTION99.93
3.7-4.070.14931430.14222734X-RAY DIFFRACTION99.97
4.07-4.660.16921280.13452761X-RAY DIFFRACTION99.97
4.66-5.870.20361450.16282775X-RAY DIFFRACTION99.9
5.87-90.310.24381390.192934X-RAY DIFFRACTION99.77

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