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- PDB-4xrg: Crystal Structure of the Homospermidine Synthase (HSS) variant H2... -

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Basic information

Entry
Database: PDB / ID: 4xrg
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant H296S from Blastochloris viridis in Complex with NAD, Putrescine and Agmatine
ComponentsHomospermidine synthase
KeywordsTRANSFERASE / homospermidine synthase / oxidoreductase / rossman fold / agmatine / 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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / ACETATE ION / AGMATINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIAMINOBUTANE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionJan 21, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: 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)107,14012
Polymers104,8562
Non-polymers2,28410
Water20,7171150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-12 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.035, 110.233, 157.474
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: 52427.824 Da / Num. of mol.: 2 / Mutation: H296S
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, 1160 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14N4
#4: Chemical ChemComp-PUT / 1,4-DIAMINOBUTANE / PUTRESCINE


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2
#5: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO3S
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / Source method: isolated from a natural source / Formula: H2O

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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: 50.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na-acetate, ammonium acetate, PEG 10000, NDSB-201, agmatine, soaked with putrescine prior flash cooling

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.06→90.306 Å / Num. all: 440552 / Num. obs: 440552 / % possible obs: 93.7 % / Redundancy: 4.4 % / Rpim(I) all: 0.088 / Rrim(I) all: 0.201 / Rsym value: 0.179 / Net I/av σ(I): 3.135 / Net I/σ(I): 3.7 / Num. measured all: 1950210
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
1.06-1.122.75.5194.5170.2132198493373.1075.5194.51710.272.5
1.12-1.1835.2344.3920.2173986572432.7815.2344.3920.288.8
1.18-1.273.54.5853.9640.2204942579592.2364.5853.9640.395.6
1.27-1.374.23.6123.1880.2234169562451.6433.6123.1880.499.4
1.37-1.54.42.0751.840.4229372519410.9312.0751.840.899.5
1.5-1.6750.9910.890.9235872471370.4260.9910.891.899.6
1.67-1.935.70.4840.4391.5238834417920.20.4840.4394.299.8
1.93-2.376.40.2410.2213226969354970.0950.2410.2219.499.9
2.37-3.356.50.0940.0867.6179296277180.0370.0940.08617.3100
3.35-110.23360.0580.05310.794572156830.0230.0580.05327.699.9

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Processing

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

4plp


Resolution: 1.3→9.999 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 12745 5.04 %Random selection by scala
Rwork0.1602 240285 --
obs0.1621 253030 99.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.36 Å2 / Biso mean: 24.5512 Å2 / Biso min: 8.71 Å2
Refinement stepCycle: LAST / Resolution: 1.3→9.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7390 0 152 1150 8692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097927
X-RAY DIFFRACTIONf_angle_d1.25810833
X-RAY DIFFRACTIONf_chiral_restr0.0681163
X-RAY DIFFRACTIONf_plane_restr0.0061423
X-RAY DIFFRACTIONf_dihedral_angle_d15.3782894
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 (%)
1.3-1.31470.39153880.37697444783293
1.3147-1.33020.40223800.36547674805495
1.3302-1.34640.38924280.36277735816397
1.3464-1.36340.38774060.35347832823898
1.3634-1.38130.37224190.34147895831498
1.3813-1.40010.34413980.31887965836399
1.4001-1.42010.34394190.30727924834399
1.4201-1.44120.32374270.29687991841899
1.4412-1.46370.32224380.27947945838399
1.4637-1.48760.31814710.27047881835299
1.4876-1.51320.28724070.24928040844799
1.5132-1.54060.30254370.23877966840399
1.5406-1.57010.2814050.22477984838999
1.5701-1.6020.27684400.21257984842499
1.602-1.63670.25744160.201380498465100
1.6367-1.67460.24664350.193580228457100
1.6746-1.71630.23954360.182980368472100
1.7163-1.76240.23694040.177680098413100
1.7624-1.8140.2014330.150680868519100
1.814-1.87220.16894060.13280848490100
1.8722-1.93860.18074200.127280738493100
1.9386-2.01570.16734330.121680418474100
2.0157-2.10660.16914310.122180918522100
2.1066-2.21650.17614280.128281238551100
2.2165-2.35370.16794690.123280738542100
2.3537-2.53270.16934400.123281368576100
2.5327-2.78250.17474000.128582108610100
2.7825-3.17390.17674290.142182278656100
3.1739-3.95710.15444510.133882528703100
3.9571-9.99930.15324510.135885138964100

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