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- PDB-6s72: Crystal Structure of the Homospermidine Synthase (HSS) variant W2... -

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Basic information

Entry
Database: PDB / ID: 6s72
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant W229A from Blastochloris viridis in Complex with NAD and PUT
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 / 1,4-DIAMINOBUTANE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 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)107,2605
Polymers105,8452
Non-polymers1,4153
Water15,547863
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-26 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.103, 109.974, 157.899
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: 52922.359 Da / Num. of mol.: 2
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: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
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: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.87→90.3481 Å / Num. obs: 86051 / % possible obs: 98.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.69 Å2 / Rrim(I) all: 0.205 / Net I/σ(I): 6.1
Reflection shellResolution: 1.87→1.9 Å / Num. unique obs: 3268

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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: 1.87→90.3481 Å / SU ML: 0.2037 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7609
RfactorNum. reflection% reflection
Rfree0.2047 4215 4.91 %
Rwork0.1615 --
obs0.1636 85778 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.44 Å2
Refinement stepCycle: LAST / Resolution: 1.87→90.3481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7396 0 94 863 8353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00867914
X-RAY DIFFRACTIONf_angle_d0.857210836
X-RAY DIFFRACTIONf_chiral_restr0.04971163
X-RAY DIFFRACTIONf_plane_restr0.00461434
X-RAY DIFFRACTIONf_dihedral_angle_d18.50172888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.890.4046770.34891631X-RAY DIFFRACTION60.74
1.89-1.920.30261350.28552613X-RAY DIFFRACTION96.25
1.92-1.940.2841440.25042770X-RAY DIFFRACTION99.9
1.94-1.960.30671380.2322702X-RAY DIFFRACTION99.93
1.96-1.990.24041500.21932709X-RAY DIFFRACTION99.97
1.99-2.020.25641390.20882719X-RAY DIFFRACTION99.97
2.02-2.050.26851430.20852705X-RAY DIFFRACTION100
2.05-2.080.28521540.19472743X-RAY DIFFRACTION99.97
2.08-2.110.22821400.18092695X-RAY DIFFRACTION100
2.11-2.140.20811550.17362750X-RAY DIFFRACTION100
2.14-2.180.22771380.16962713X-RAY DIFFRACTION100
2.18-2.220.22331490.16792757X-RAY DIFFRACTION100
2.22-2.260.22711390.16042721X-RAY DIFFRACTION99.97
2.26-2.310.22941670.16422716X-RAY DIFFRACTION99.97
2.31-2.360.20071490.15492710X-RAY DIFFRACTION99.97
2.36-2.410.22031420.15292760X-RAY DIFFRACTION100
2.41-2.470.21561270.15022734X-RAY DIFFRACTION99.97
2.47-2.540.18441430.14392749X-RAY DIFFRACTION99.97
2.54-2.620.18921420.14622789X-RAY DIFFRACTION100
2.62-2.70.20921460.15992713X-RAY DIFFRACTION100
2.7-2.80.22051240.15672780X-RAY DIFFRACTION100
2.8-2.910.18321540.15572765X-RAY DIFFRACTION100
2.91-3.040.17981250.15492775X-RAY DIFFRACTION100
3.04-3.20.22771430.15882781X-RAY DIFFRACTION100
3.2-3.40.2161310.15882787X-RAY DIFFRACTION100
3.4-3.660.17751490.14952783X-RAY DIFFRACTION100
3.66-4.030.14821500.13342802X-RAY DIFFRACTION100
4.03-4.620.14591330.1262835X-RAY DIFFRACTION100
4.62-5.820.15991490.13772855X-RAY DIFFRACTION99.93
5.82-90.34810.25521400.17853001X-RAY DIFFRACTION99.62

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