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

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Basic information

Entry
Database: PDB / ID: 4plp
TitleCrystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD
ComponentsHomospermidine synthase
KeywordsTRANSFERASE / homospermidine synthase / oxidoreductase / rossman 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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 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
DepositionMay 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)107,3475
Polymers105,9612
Non-polymers1,3863
Water18,6461035
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-36 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.045, 109.792, 192.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O32323, homospermidine synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1035 / 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: 3.5 Å3/Da / Density % sol: 64.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na-acetate, ammoniumacetate, PEG 3350, PEG400 as cryoprotectant

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 12, 2011
RadiationMonochromator: Si111 DCM with sagital bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.314→96.478 Å / Num. all: 307932 / Num. obs: 307932 / % possible obs: 87.5 % / Redundancy: 3.5 % / Rpim(I) all: 0.112 / Rrim(I) all: 0.215 / Rsym value: 0.182 / Net I/av σ(I): 3.456 / Net I/σ(I): 4.5 / Num. measured all: 1068673
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
1.31-1.382.39.3357.3170.154142232675.6939.3357.31710.145.8
1.38-1.472.85.5654.540.298674347593.1555.5654.540.272.3
1.47-1.573.53.0422.580.3153898441121.5933.0422.580.497.3
1.57-1.73.71.8261.5660.5157161421020.9331.8261.5660.899.4
1.7-1.863.71.1540.9890.7144999388140.591.1540.9891.699.5
1.86-2.083.70.6040.5161.3131102352390.3110.6040.5163.499.6
2.08-2.43.70.3220.2752.4116723311680.1660.3220.2756.599.6
2.4-2.943.70.1480.1265.498024264210.0760.1480.12610.799.4
2.94-4.153.60.070.05911.373717204860.0360.070.05918.898.9
4.15-47.7133.50.0460.03914.840233115640.0240.0460.0392498.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å47.59 Å
Translation3 Å47.59 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
MOLREPphasing
ARPmodel building
PDB_EXTRACT3.11data extraction
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PH5
Resolution: 1.49→9.996 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2254 11959 5.03 %
Rwork0.1906 225951 -
obs0.1924 237910 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.32 Å2 / Biso mean: 31.2906 Å2 / Biso min: 9.99 Å2
Refinement stepCycle: LAST / Resolution: 1.49→9.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 92 1035 8541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127887
X-RAY DIFFRACTIONf_angle_d1.41310796
X-RAY DIFFRACTIONf_chiral_restr0.0811166
X-RAY DIFFRACTIONf_plane_restr0.0071420
X-RAY DIFFRACTIONf_dihedral_angle_d15.1342883
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 (%)
1.49-1.50690.39883250.3966569689487
1.5069-1.52450.39633900.38497220761095
1.5245-1.54310.38824090.37077408781798
1.5431-1.56250.37763630.36657513787699
1.5625-1.5830.40414160.36047429784599
1.583-1.60460.37494140.35547502791699
1.6046-1.62740.33943950.33397554794999
1.6274-1.65160.37164010.33227474787599
1.6516-1.67730.34474070.33187494790199
1.6773-1.70470.33353860.33387522790899
1.7047-1.73390.34654100.32347521793199
1.7339-1.76530.33283940.30897571796599
1.7653-1.79910.34344240.29347580800499
1.7991-1.83560.323970.28387544794199
1.8356-1.87520.30294110.27967516792799
1.8752-1.91850.31633660.2817586795299
1.9185-1.96620.3023770.26677589796699
1.9662-2.01890.23354020.216175927994100
2.0189-2.07780.24764130.20637607802099
2.0778-2.14420.25294160.19375657981100
2.1442-2.22010.20614060.178375897995100
2.2201-2.30790.21664060.17177615802199
2.3079-2.41150.20074040.16247632803699
2.4115-2.53670.20764110.15387597800899
2.5367-2.69270.19074210.15167625804699
2.6927-2.8960.20213990.15147640803999
2.896-3.17880.16723820.15297675805799
3.1788-3.61960.18024140.14577620803499
3.6196-4.49040.1633840.12777710809498
4.4904-9.99640.16274160.13297892830898

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