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- PDB-4xq9: Crystal Structure of the Homospermidine Synthase (HSS) from Blast... -

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Basic information

Entry
Database: PDB / ID: 4xq9
TitleCrystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD
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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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)106,4036
Polymers104,9582
Non-polymers1,4454
Water23,5461307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-31 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.057, 110.675, 157.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-1193-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Homospermidine synthase / HSS


Mass: 52478.891 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
#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-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 1307 / 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: 50.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Na-acetate, ammonium acetate, PEG 10000, NDSB-201, 1,5-diaminopentane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.51→90.552 Å / Num. all: 133537 / Num. obs: 133537 / % possible obs: 80.9 % / Redundancy: 5.5 % / Rpim(I) all: 0.099 / Rrim(I) all: 0.247 / Rsym value: 0.225 / Net I/av σ(I): 3.029 / Net I/σ(I): 6 / Num. measured all: 737330
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.51-1.591.77.1325.2010.1867849764.8447.1325.2010.121.1
1.59-1.692.23.3382.5430.329000129742.1253.3382.5430.358.1
1.69-1.82.92.0051.6330.553480183901.1322.0051.6330.686.9
1.8-1.954.41.2771.1240.786408196940.5951.2771.1241.499.4
1.95-2.147.20.8480.7860.9131619183190.3150.8480.7863.7100
2.14-2.397.40.5130.4771.4123055165910.1880.5130.4775.8100
2.39-2.767.40.2890.2692.5108686146850.1060.2890.2698.1100
2.76-3.387.30.1460.1355.290948125110.0540.1460.13512.9100
3.38-4.776.90.0840.0788.76800997900.0320.0840.07820.7100
4.77-47.7536.70.0630.05810.93744756070.0240.0630.05819.999.8

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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: 1.6→9.989 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 6224 4.98 %Random selection by scala
Rwork0.1614 118848 --
obs0.1635 125072 90.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.28 Å2 / Biso mean: 25.5583 Å2 / Biso min: 9.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→9.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7398 0 96 1307 8801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087813
X-RAY DIFFRACTIONf_angle_d1.14910686
X-RAY DIFFRACTIONf_chiral_restr0.0451155
X-RAY DIFFRACTIONf_plane_restr0.0051403
X-RAY DIFFRACTIONf_dihedral_angle_d14.422842
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 (%)
1.6-1.61810.3662520.37871263131529
1.6181-1.63710.3721060.36151979208546
1.6371-1.65690.3527930.36212417251055
1.6569-1.67780.39021440.35892827297165
1.6778-1.69980.37771840.35283075325972
1.6998-1.7230.33111800.33173432361279
1.723-1.74750.35072020.31753692389486
1.7475-1.77340.33422000.31983905410589
1.7734-1.80090.33722430.30274081432495
1.8009-1.83030.33352080.27924244445297
1.8303-1.86170.32052160.26834289450599
1.8617-1.89530.27912270.24843384565100
1.8953-1.93150.27312230.242543614584100
1.9315-1.97060.24642330.206643394572100
1.9706-2.01310.23022440.176243814625100
2.0131-2.05960.24822370.16343324569100
2.0596-2.11060.18962170.150143384555100
2.1106-2.16710.18961950.135744254620100
2.1671-2.23020.18032190.134843694588100
2.2302-2.30130.17112200.137444054625100
2.3013-2.38250.19432490.138243224571100
2.3825-2.47650.19872620.131743574619100
2.4765-2.58730.18242410.130843954636100
2.5873-2.72110.20862390.134244154654100
2.7211-2.88780.17212240.140943724596100
2.8878-3.10450.19322340.142644294663100
3.1045-3.40560.19051940.134144744668100
3.4056-3.87310.14392180.12244724690100
3.8731-4.78850.1542670.108544924759100
4.7885-9.98950.16062530.140246284881100

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