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- PDB-4xr4: Crystal Structure of the Homospermidine Synthase (HSS) from Blast... -

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Basic information

Entry
Database: PDB / ID: 4xr4
TitleCrystal Structure of the Homospermidine Synthase (HSS) from Blastochloris viridis in Complex with NAD and Agmatine
ComponentsHomospermidine synthase
KeywordsTRANSFERASE / homospermidine synthase / oxidoreductase / rossman fold / agmatine
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: 1.626 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 20, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)108,36923
Polymers104,9902
Non-polymers3,37921
Water17,727984
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-59 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.857, 108.555, 161.323
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: 52494.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MET-199 is oxidized to MHO / 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, 1005 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14N4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 984 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Na-acetate, ammonium acetate, PEG 10000, NDSB-201, agmatine

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 1.626→90.063 Å / Num. all: 119777 / Num. obs: 119777 / % possible obs: 98.2 % / Redundancy: 6.3 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Rsym value: 0.089 / Net I/av σ(I): 7.769 / Net I/σ(I): 14.1 / Num. measured all: 759636
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
1.63-1.714.80.8340.745174969155540.3640.8340.745288.2
1.71-1.826.50.6310.581.3108823166540.2460.6310.583.2100
1.82-1.946.60.3930.3622.1102911156730.1530.3930.3625.1100
1.94-2.16.60.2380.2193.596485146350.0920.2380.2198.1100
2.1-2.36.60.1570.1455.388865134980.0610.1570.14511.9100
2.3-2.576.50.1120.1037.379635122320.0430.1120.10315.999.9
2.57-2.976.70.0790.07310.372912108630.030.0790.07321.9100
2.97-3.636.70.0480.04415.96203292480.0180.0480.04433.899.9
3.63-5.146.60.0360.03419.84751572330.0140.0360.03444.299.9
5.14-161.3236.10.0350.03219.72548941870.0140.0350.03242.499.8

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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: 1.626→9.998 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1711 5986 5.03 %
Rwork0.1364 113081 -
obs0.1381 119067 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.48 Å2 / Biso mean: 22.8389 Å2 / Biso min: 7.74 Å2
Refinement stepCycle: LAST / Resolution: 1.626→9.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7400 0 219 984 8603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.027922
X-RAY DIFFRACTIONf_angle_d1.33710818
X-RAY DIFFRACTIONf_chiral_restr0.0481160
X-RAY DIFFRACTIONf_plane_restr0.0061415
X-RAY DIFFRACTIONf_dihedral_angle_d15.9162866
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 (%)
1.6256-1.6440.26931020.26761942204451
1.644-1.66330.27191940.23253732392698
1.6633-1.68350.24481940.21913744393899
1.6835-1.70470.26731950.209137703965100
1.7047-1.7270.21872060.191838094015100
1.727-1.75050.21712040.185237833987100
1.7505-1.77540.21431930.180238374030100
1.7754-1.80170.20932050.171237613966100
1.8017-1.82970.19922230.167138174040100
1.8297-1.85950.21891700.164238053975100
1.8595-1.89140.20451860.157738604046100
1.8914-1.92550.19582230.147137373960100
1.9255-1.96230.20042060.142838354041100
1.9623-2.0020.16442020.13637893991100
2.002-2.04520.16851920.13438294021100
2.0452-2.09240.17822130.129338184031100
2.0924-2.14420.16791930.127738254018100
2.1442-2.20160.18131960.121238294025100
2.2016-2.26560.17312000.115138444044100
2.2656-2.33790.14251910.118338244015100
2.3379-2.42030.15362390.115537854024100
2.4203-2.51570.15632250.113338284053100
2.5157-2.62820.15112190.112838474066100
2.6282-2.7640.14181920.123538654057100
2.764-2.93310.17722030.122538694072100
2.9331-3.15290.15831950.131538784073100
3.1529-3.45830.16411720.125139104082100
3.4583-3.93180.14282270.121839154142100
3.9318-4.85720.13522110.117339334144100
4.8572-9.99860.19632150.165440614276100

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