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- PDB-6s65: Crystal Structure of the Homospermidine Synthase (HSS) variant N1... -

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Basic information

Entry
Database: PDB / ID: 6s65
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant N135F 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHelfrich, F. / Scheidig, A.J.
CitationJournal: To Be Published
Title: Crystal Structure of the Homospermidine Synthase (HSS) variant N135F from Blastochloris viridis in Complex with NAD
Authors: Scheidig, A.J. / Helfrich, F.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Homospermidine synthase
B: Homospermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4684
Polymers106,1412
Non-polymers1,3272
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-29 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.703, 110.401, 159.541
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: 53070.562 Da / Num. of mol.: 2 / Mutation: N135F, 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: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.56 Å3/Da / Density % sol: 51.96 %
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: 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: 1.66→90.784 Å / Num. obs: 115829 / % possible obs: 90.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.07 Å2 / Rrim(I) all: 0.196 / Net I/σ(I): 5.1
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 1105

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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: 1.75→90.784 Å / SU ML: 0.2537 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.8132
RfactorNum. reflection% reflection
Rfree0.2172 5333 5.01 %
Rwork0.1804 --
obs0.1822 106405 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.92 Å2
Refinement stepCycle: LAST / Resolution: 1.75→90.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7265 0 88 599 7952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957666
X-RAY DIFFRACTIONf_angle_d0.899810482
X-RAY DIFFRACTIONf_chiral_restr0.05921135
X-RAY DIFFRACTIONf_plane_restr0.00591377
X-RAY DIFFRACTIONf_dihedral_angle_d20.57282782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.43381410.40482726X-RAY DIFFRACTION80.76
1.77-1.790.38921720.38393054X-RAY DIFFRACTION89.56
1.79-1.810.40191720.35663320X-RAY DIFFRACTION97.84
1.81-1.840.35331610.33413388X-RAY DIFFRACTION98.09
1.84-1.860.3711990.30223285X-RAY DIFFRACTION98.03
1.86-1.890.31311670.29413362X-RAY DIFFRACTION98.19
1.89-1.910.28451660.27533330X-RAY DIFFRACTION98.17
1.91-1.940.31941610.26963391X-RAY DIFFRACTION98.12
1.94-1.970.28641900.25453352X-RAY DIFFRACTION98.2
1.97-20.27161790.23263346X-RAY DIFFRACTION98.35
2-2.040.26671680.20183336X-RAY DIFFRACTION98.48
2.04-2.070.24431720.1963355X-RAY DIFFRACTION98.16
2.07-2.110.23111770.19123342X-RAY DIFFRACTION97.37
2.11-2.160.24541650.18943369X-RAY DIFFRACTION97.49
2.16-2.20.24231810.19073332X-RAY DIFFRACTION98.35
2.2-2.260.24321840.1853410X-RAY DIFFRACTION98.76
2.26-2.310.2311630.17953395X-RAY DIFFRACTION99.05
2.31-2.380.22231790.17613376X-RAY DIFFRACTION99.05
2.38-2.440.21921760.17623421X-RAY DIFFRACTION98.87
2.44-2.520.22261840.16953399X-RAY DIFFRACTION98.98
2.52-2.610.22691990.16953376X-RAY DIFFRACTION99.33
2.61-2.720.22881920.18123408X-RAY DIFFRACTION99.23
2.72-2.840.25231860.17873422X-RAY DIFFRACTION99.31
2.84-2.990.22891990.17653442X-RAY DIFFRACTION99.18
2.99-3.180.20611820.17993429X-RAY DIFFRACTION99.07
3.18-3.430.18661760.16543457X-RAY DIFFRACTION99.64
3.43-3.770.16691820.1533487X-RAY DIFFRACTION99.67
3.77-4.320.17131860.13823523X-RAY DIFFRACTION99.7
4.32-5.440.15351880.13583534X-RAY DIFFRACTION99.81
5.44-90.7840.20731860.17813705X-RAY DIFFRACTION99.11

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