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- PDB-6s49: Crystal Structure of the Homospermidine Synthase (HSS) variant E2... -

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Basic information

Entry
Database: PDB / ID: 6s49
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant E210A 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
AGMATINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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_chem_comp_depositor_info / pdbx_chem_comp_instance_depositor_info / pdbx_data_processing_status / pdbx_database_proc / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_id / _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 / _pdbx_chem_comp_depositor_info.comp_id / _pdbx_chem_comp_depositor_info.name / _pdbx_chem_comp_instance_depositor_info.comp_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id
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)107,7388
Polymers105,9592
Non-polymers1,7796
Water19,9251106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-57 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.980, 109.822, 157.281
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: 52979.457 Da / Num. of mol.: 2
Mutation: E210A, G1 and P2 belong to protease restriction site, G4 was inserted
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-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14N4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1106 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
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: 1.69→90.04 Å / Num. obs: 115391 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rrim(I) all: 0.23 / Net I/σ(I): 5.8
Reflection shellResolution: 1.69→1.72 Å / Num. unique obs: 4205

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Processing

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

4plp


Resolution: 1.69→63.938 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.64
RfactorNum. reflection% reflection
Rfree0.1862 5670 4.92 %
Rwork0.1549 --
obs0.1564 115162 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.69→63.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7390 0 116 1106 8612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117790
X-RAY DIFFRACTIONf_angle_d1.05810647
X-RAY DIFFRACTIONf_dihedral_angle_d21.042783
X-RAY DIFFRACTIONf_chiral_restr0.4651148
X-RAY DIFFRACTIONf_plane_restr0.0061395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6903-1.70950.36011220.3212272X-RAY DIFFRACTION62
1.7095-1.72960.34341960.2543525X-RAY DIFFRACTION97
1.7296-1.75070.24672010.21773636X-RAY DIFFRACTION100
1.7507-1.77290.22251770.20253683X-RAY DIFFRACTION100
1.7729-1.79620.2321940.19213651X-RAY DIFFRACTION100
1.7962-1.82080.24271850.18473652X-RAY DIFFRACTION100
1.8208-1.84680.2341810.18563661X-RAY DIFFRACTION100
1.8468-1.87440.21631970.17483684X-RAY DIFFRACTION100
1.8744-1.90370.20221810.17163626X-RAY DIFFRACTION100
1.9037-1.93490.22732030.17543725X-RAY DIFFRACTION100
1.9349-1.96830.19621710.17073630X-RAY DIFFRACTION100
1.9683-2.00410.19241960.16063678X-RAY DIFFRACTION100
2.0041-2.04260.1821800.15143662X-RAY DIFFRACTION100
2.0426-2.08430.19121790.14733691X-RAY DIFFRACTION100
2.0843-2.12970.19692290.14753655X-RAY DIFFRACTION100
2.1297-2.17920.17731720.14163671X-RAY DIFFRACTION100
2.1792-2.23370.16241910.14193703X-RAY DIFFRACTION100
2.2337-2.29410.17371820.14213683X-RAY DIFFRACTION100
2.2941-2.36160.18662030.14023670X-RAY DIFFRACTION100
2.3616-2.43780.18811980.14133684X-RAY DIFFRACTION100
2.4378-2.5250.17171990.13263686X-RAY DIFFRACTION100
2.525-2.62610.17232120.1323710X-RAY DIFFRACTION100
2.6261-2.74560.1781750.14053714X-RAY DIFFRACTION100
2.7456-2.89030.17941840.14623718X-RAY DIFFRACTION100
2.8903-3.07140.17931760.15443744X-RAY DIFFRACTION100
3.0714-3.30860.19172010.15613738X-RAY DIFFRACTION100
3.3086-3.64150.16391840.14283746X-RAY DIFFRACTION100
3.6415-4.16830.14682110.13343777X-RAY DIFFRACTION100
4.1683-5.25130.1512020.13013813X-RAY DIFFRACTION100
5.2513-63.98410.19021880.18584004X-RAY DIFFRACTION100

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