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- PDB-4tvb: Crystal Structure of the Homospermidine Synthase (HSS) from Blast... -

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Basic information

Entry
Database: PDB / ID: 4tvb
TitleCrystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD, Putrescine and sym-Homospermidine
ComponentsHomospermidine synthase
KeywordsTRANSFERASE / homospermidine synthase / oxidoreductase / rossman fold
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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / sym-homospermidine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 1,4-DIAMINOBUTANE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.689 Å
AuthorsKrossa, S.
CitationJournal: Sci Rep / Year: 2016
Title: Comprehensive Structural Characterization of the Bacterial Homospermidine Synthase-an Essential Enzyme of the Polyamine Metabolism.
Authors: Krossa, S. / Faust, A. / Ober, D. / Scheidig, A.J.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)107,7387
Polymers105,9612
Non-polymers1,7785
Water23,3831298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-23 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.510, 109.254, 157.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Homospermidine synthase / HSS


Mass: 52980.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastochloris viridis (bacteria) / Gene: hss / Plasmid: pETM14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O32323, homospermidine synthase

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Non-polymers , 6 types, 1303 molecules

#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-37Z / sym-homospermidine


Mass: 159.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H21N3
#4: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO3S
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1298 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAccording to the author the molecule 37Z present in the entry depicts the transition state between ...According to the author the molecule 37Z present in the entry depicts the transition state between the oxidised sym-homospermidine and its regular form. The author also suggest that ligand PUT is representing a transition state between 1,4-diaminobutane and non-hydrolysed 4-aminobutanal.

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Na-acetate, ammoniumacetate, PEG 10000, NDSB-201, 1,3-diaminopropane
PH range: 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 1.689→89.717 Å / Num. all: 113442 / Num. obs: 113442 / % possible obs: 98.1 % / Redundancy: 12.8 % / Rpim(I) all: 0.072 / Rrim(I) all: 0.262 / Rsym value: 0.252 / Net I/av σ(I): 2.8 / Net I/σ(I): 8.6 / Num. measured all: 1454896
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.689-1.789.72.2282.1120.4141189144970.6912.2282.11210.987.1
1.78-1.8913.31.7281.6620.5209603158130.471.7281.6621.5100
1.89-2.0213.31.0951.0530.7197812148820.2981.0951.0532.5100
2.02-2.1813.40.6980.6721.1185941139210.1890.6980.6724.1100
2.18-2.3913.30.4770.4581.7169958127840.130.4770.4585.9100
2.39-2.6713.10.3250.3132.5152660116190.0890.3250.3138.3100
2.67-3.0813.50.2080.23.8139362102970.0560.2080.212.6100
3.08-3.7813.50.1050.1017.411888087860.0280.1050.10123100
3.78-5.3413.20.0730.07110.29093868720.020.0730.07131.2100
5.34-109.25412.20.0680.06510.44855339710.0190.0680.06530.699.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PLP

4plp


Resolution: 1.689→9.988 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 5652 5.02 %Random selection
Rwork0.1787 106898 --
obs0.1802 112550 97.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.83 Å2 / Biso mean: 23.1095 Å2 / Biso min: 7.24 Å2
Refinement stepCycle: LAST / Resolution: 1.689→9.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7416 0 118 1298 8832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057780
X-RAY DIFFRACTIONf_angle_d1.110627
X-RAY DIFFRACTIONf_chiral_restr0.0351147
X-RAY DIFFRACTIONf_plane_restr0.0111391
X-RAY DIFFRACTIONf_dihedral_angle_d13.8392819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.689-1.70820.3666940.33061569166344
1.7082-1.72820.36121770.32313418359596
1.7282-1.74920.30341860.29363574376099
1.7492-1.77120.28821960.292435693765100
1.7712-1.79430.30081930.279936203813100
1.7943-1.81880.32841740.273936023776100
1.8188-1.84460.28532090.262835833792100
1.8446-1.8720.27821700.253736453815100
1.872-1.9010.27852100.245935693779100
1.901-1.9320.2582100.243235913801100
1.932-1.9650.24241680.225836173785100
1.965-2.00050.24782150.209235903805100
2.0005-2.03870.20961890.199936153804100
2.0387-2.07990.20921690.192636343803100
2.0799-2.12470.23671890.188236463835100
2.1247-2.17360.21982180.179735533771100
2.1736-2.22740.2051690.176336733842100
2.2274-2.28690.19261890.173136183807100
2.2869-2.35340.24231760.177336373813100
2.3534-2.42830.18572080.172436233831100
2.4283-2.51370.20682070.167836163823100
2.5137-2.61270.20761880.169636573845100
2.6127-2.72930.21472160.172536373853100
2.7293-2.86990.21051850.167136483833100
2.8699-3.04490.20451630.163636973860100
3.0449-3.27230.1831860.158636973883100
3.2723-3.58770.1661970.143236853882100
3.5877-4.07570.15241970.140136973894100
4.0757-5.02370.14151910.133137693960100
5.0237-9.98790.20532130.171838494062100

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