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- PDB-6s3x: Crystal Structure of the Homospermidine Synthase (HSS) variant E2... -

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Basic information

Entry
Database: PDB / ID: 6s3x
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant E210Q 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 / oxidoreductase 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: 1.72 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 26, 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)107,8528
Polymers106,0732
Non-polymers1,7796
Water15,241846
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-54 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.325, 110.100, 158.153
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: 53036.508 Da / Num. of mol.: 2 / Mutation: E210Q
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE / Agmatine


Mass: 130.191 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C5H14N4
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
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: 0.9789 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.66→90.36 Å / Num. obs: 111532 / % possible obs: 89.5 % / Redundancy: 7 % / Rrim(I) all: 0.197 / Net I/σ(I): 6.4
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 1004

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Cootmodel building
pointlessdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLP
Resolution: 1.72→90.36 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.45
RfactorNum. reflection% reflection
Rfree0.1946 5348 5 %
Rwork0.163 --
obs0.1646 107034 95.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→90.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7398 0 116 846 8360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117841
X-RAY DIFFRACTIONf_angle_d1.14210722
X-RAY DIFFRACTIONf_dihedral_angle_d18.8292810
X-RAY DIFFRACTIONf_chiral_restr0.4651152
X-RAY DIFFRACTIONf_plane_restr0.0061407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.73950.30951160.30442446X-RAY DIFFRACTION70
1.7395-1.760.34691250.29492613X-RAY DIFFRACTION74
1.76-1.78150.33271500.28922880X-RAY DIFFRACTION81
1.7815-1.8040.35291580.28093340X-RAY DIFFRACTION94
1.804-1.82780.3161680.27293422X-RAY DIFFRACTION96
1.8278-1.85280.29821570.25943401X-RAY DIFFRACTION96
1.8528-1.87930.30871990.23913384X-RAY DIFFRACTION97
1.8793-1.90730.26081750.24123418X-RAY DIFFRACTION97
1.9073-1.93710.25942160.23383370X-RAY DIFFRACTION97
1.9371-1.96890.24351830.22143424X-RAY DIFFRACTION97
1.9689-2.00290.26071550.20693457X-RAY DIFFRACTION97
2.0029-2.03930.2371840.19843418X-RAY DIFFRACTION97
2.0393-2.07850.24921850.18753435X-RAY DIFFRACTION97
2.0785-2.12090.24331880.17933428X-RAY DIFFRACTION97
2.1209-2.16710.21831820.17353449X-RAY DIFFRACTION97
2.1671-2.21750.22141860.15763441X-RAY DIFFRACTION98
2.2175-2.27290.20311880.15453424X-RAY DIFFRACTION98
2.2729-2.33440.17442010.15783478X-RAY DIFFRACTION98
2.3344-2.40310.19481630.1553492X-RAY DIFFRACTION98
2.4031-2.48070.19951870.15253466X-RAY DIFFRACTION98
2.4807-2.56930.19141910.1423491X-RAY DIFFRACTION98
2.5693-2.67220.19181930.14423502X-RAY DIFFRACTION98
2.6722-2.79380.18381990.14533499X-RAY DIFFRACTION99
2.7938-2.94110.17471870.14973516X-RAY DIFFRACTION99
2.9411-3.12540.21121940.15333471X-RAY DIFFRACTION97
3.1254-3.36670.20231580.15023586X-RAY DIFFRACTION98
3.3667-3.70550.17431630.1443593X-RAY DIFFRACTION99
3.7055-4.24170.14712000.1283584X-RAY DIFFRACTION99
4.2417-5.34410.1352110.11993595X-RAY DIFFRACTION98
5.3441-90.4850.15021860.16823663X-RAY DIFFRACTION95

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