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- PDB-4xqg: Crystal Structure of the Homospermidine Synthase (HSS) variant E2... -

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Basic information

Entry
Database: PDB / ID: 4xqg
TitleCrystal Structure of the Homospermidine Synthase (HSS) variant E237Q 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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / ACETATE ION / AGMATINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Homospermidine synthase
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.417 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 1.1Mar 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)108,16218
Polymers105,1862
Non-polymers2,97616
Water20,6451146
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-52 kcal/mol
Surface area32720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.809, 109.250, 157.640
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: 52592.992 Da / Num. of mol.: 2 / Mutation: E237Q
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, 1162 molecules

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


Mass: 663.425 Da / Num. of mol.: 2 / Mutation: E237Q
Source method: isolated from a genetically manipulated source
Formula: C21H27N7O14P2 / Source: (gene. exp.) Blastochloris viridis (bacteria) / Gene: hss / Plasmid: pETM14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: homospermidine synthase / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11NO3S
#5: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14N4
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1146 / 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: 49.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Na-acetate, ammoniumacetate, PEG 10000, NDSB-201, agmatine, 1,4-diaminobutane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.417→89.794 Å / Num. all: 189622 / Num. obs: 189622 / % possible obs: 96.9 % / Redundancy: 6.6 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Rsym value: 0.095 / Net I/av σ(I): 6.25 / Net I/σ(I): 10.9 / Num. measured all: 1246679
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
1.417-1.495.50.9760.8860.9133514241470.3980.9760.88611.685.5
1.49-1.586.80.7240.6691.1180235264910.2730.7240.6692.698.7
1.58-1.696.60.5050.4661.7162281246150.1930.5050.4663.697.8
1.69-1.836.90.3410.3162.4160173233450.1280.3410.3165.499.1
1.83-26.50.2070.194140507214690.0790.2070.198.398.8
2-2.246.90.130.126.2135501195290.0490.130.1213.399.4
2.24-2.596.60.0950.0888.2114110172090.0360.0950.08817.398.7
2.59-3.1770.0680.06310.9102797147710.0260.0680.06324.399.5
3.17-4.486.60.0470.04314.475380114600.0180.0470.04335.598.9
4.48-109.256.40.0420.03815.24218165860.0160.0420.03836.399

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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: 1.417→9.997 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1611 9510 5.03 %Random selection by scala
Rwork0.1287 179402 --
obs0.1303 188912 96.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.5 Å2 / Biso mean: 20.6238 Å2 / Biso min: 8.24 Å2
Refinement stepCycle: LAST / Resolution: 1.417→9.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7407 0 193 1146 8746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097965
X-RAY DIFFRACTIONf_angle_d1.36310886
X-RAY DIFFRACTIONf_chiral_restr0.2571167
X-RAY DIFFRACTIONf_plane_restr0.0061423
X-RAY DIFFRACTIONf_dihedral_angle_d14.4392888
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 (%)
1.4169-1.4330.34741790.29453426360556
1.433-1.44980.27273050.25845312561787
1.4498-1.46740.27273100.23495784609494
1.4674-1.48590.26653450.21135962630798
1.4859-1.50540.24213240.19346006633098
1.5054-1.52590.22753250.18616015634098
1.5259-1.54770.22733270.17276070639799
1.5477-1.57070.19813090.16336069637899
1.5707-1.59510.18463060.14956054636099
1.5951-1.62120.18363130.14816070638398
1.6212-1.6490.18373290.14645857618696
1.649-1.67890.18913190.13695940625997
1.6789-1.7110.17783220.12776120644299
1.711-1.74570.17882770.1256092636999
1.7457-1.78350.17273150.11866119643499
1.7835-1.82470.16233130.11736139645299
1.8247-1.87010.14753130.11256077639099
1.8701-1.92030.14683240.10956103642799
1.9203-1.97640.14483190.11146040635998
1.9764-2.03970.14843250.10656128645399
2.0397-2.11190.14393220.10746149647199
2.1119-2.19560.14413370.10486130646799
2.1956-2.29440.14153290.10576157648699
2.2944-2.41370.14663330.10756153648699
2.4137-2.56260.13873370.10766016635397
2.5626-2.75660.15463090.119962536562100
2.7566-3.0270.15853480.136192654099
3.027-3.44920.15153340.13116266660099
3.4492-4.28780.14023300.1226240657098
4.2878-9.99770.15533320.13696463679599

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