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- PDB-1xj5: X-RAY STRUCTURE OF SPERMIDINE SYNTHASE FROM ARABIDOPSIS THALIANA ... -

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Basic information

Entry
Database: PDB / ID: 1xj5
TitleX-RAY STRUCTURE OF SPERMIDINE SYNTHASE FROM ARABIDOPSIS THALIANA GENE AT1G23820
ComponentsSpermidine synthase 1
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / AT1G23820 / PUTRESCINE AMINOPROPYL TRANSFERASE / SPERMIDINE SYNTHASE / SPDS1 / POLYAMINE / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytosol
Similarity search - Function
Spermidine/spermine synthase, eukaryotes / Spermidine synthase, tetramerisation domain / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. ...Spermidine/spermine synthase, eukaryotes / Spermidine synthase, tetramerisation domain / Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain / Spermidine Synthase; Chain: A, domain 2 / Vaccinia Virus protein VP39 / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Spermidine synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 2.7 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: X-RAY STRUCTURE OF SPERMIDINE SYNTHASE FROM ARABIDOPSIS THALIANA GENE AT1G23820
Authors: Center for Eukaryotic Structural Genomics
History
DepositionSep 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spermidine synthase 1
B: Spermidine synthase 1
C: Spermidine synthase 1
D: Spermidine synthase 1


Theoretical massNumber of molelcules
Total (without water)147,6864
Polymers147,6864
Non-polymers00
Water10,377576
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.814, 95.207, 89.164
Angle α, β, γ (deg.)90.00, 104.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains a tetramer representing the complete biological unit.

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Components

#1: Protein
Spermidine synthase 1 / Putrescine aminopropyltransferase 1 / SPDSY 1


Mass: 36921.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT1G23820 / Plasmid: pVP-16 / Production host: Escherichia coli (E. coli) / Strain (production host): pLacI+RARE / References: UniProt: Q9ZUB3, spermidine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10 MG/ML PROTEIN, 24 PERCENT MEPEG 2K, 0.160 M POTASSIUM GLUTAMATE, 0.100M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å
DetectorType: APS-1 / Detector: CCD / Date: Jul 31, 2004
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator: water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.66→26.29 Å / Num. obs: 39682 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 45.1 Å2 / Limit h max: 32 / Limit h min: -33 / Limit k max: 35 / Limit k min: -33 / Limit l max: 33 / Limit l min: 0 / Observed criterion F max: 238434.4 / Observed criterion F min: 0.225 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
2.7-2.765.10.3384.126400.97796.3
2.76-2.830.29526760.91798.3
2.83-2.910.25826840.9198.1
2.91-2.990.23326620.93898.3
2.99-3.090.19826500.97598.1
3.09-3.20.17326410.98198
3.2-3.330.1332673197.7
3.33-3.480.10626470.94997.5
3.48-3.660.07926490.86897.3
3.66-3.890.06926420.93697.2
3.89-4.190.05626560.78696.7
4.19-4.620.04926180.90796.2
4.62-5.280.05126470.94795.9
5.28-6.650.06226250.9895.2
6.65-500.05725881.03891.9

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Phasing

Phasing
Method
SAD
molecular replacement
Phasing MADD res high: 4.49 Å / D res low: 26.3 Å / FOM : 0.374 / FOM acentric: 0.384 / FOM centric: 0 / Reflection: 15682
Phasing MAD setR cullis: 0.644 / R cullis acentric: 0.636 / R cullis centric: 10 / R kraut: 0.029 / R kraut acentric: 0.029 / R kraut centric: 0.008 / Highest resolution: 4.49 Å / Lowest resolution: 26.3 Å / FOM : 0.38 / FOM acentric: 0.39 / FOM centric: 0 / Loc: 1.781 / Loc acentric: 1.781 / Loc centric: 1.84 / Power: 1.66 kW / Power acentric: 1.661 / Power centric: 1.631
Phasing MAD setWavelength: 0.97935 Å / Atom type: SE / F double prime refined: -0.3 / F prime refined: -11
Phasing MAD set shell

ID: f_peak_FRIED / R cullis centric: 10 / FOM centric: 0

Resolution (Å)R cullisR cullis acentricR krautR kraut acentricR kraut centricFOM FOM acentricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
8.88-26.30.6130.60.0280.0280.010.3910.4082.2282.2312.231.7361.741.637
7.09-8.880.6170.6080.0310.0320.0090.3890.4011.9431.9441.9431.7271.7291.696
6.21-7.090.6010.5930.0340.0350.0090.4210.4321.8551.8561.8561.7461.7551.389
5.65-6.210.6380.6320.0330.0340.0060.3890.3971.6421.6431.6431.731.7291.777
5.25-5.650.6790.6720.0320.0320.0090.3710.3781.7131.7141.7131.5961.5981.503
4.94-5.250.7040.6960.0270.0280.0080.3620.371.6461.6461.6461.5451.5371.883
4.69-4.940.6680.6620.0240.0240.0090.3730.381.621.621.621.5721.5691.743
4.49-4.690.7170.7090.0240.0240.0020.3480.3561.6151.6151.6151.4881.491.395
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
135.834714.987529.4728SE59.40441
260.95661.195640.3866SE95.88061
336.927254.18219.72706SE93.53731
452.716861.395522.8366SE68.58751
561.100625.46818.4485SE98.40921
633.663712.688615.6467SE103.1431
765.107131.9665.93087SE63.49861
836.114782.488134.9378SE95.04221
950.40931.615625.6029SE58.0561
1048.641981.476228.6627SE66.68341
1114.2359-0.43814517.2648SE89.88391
1249.450886.694815.1876SE64.43081
1378.378432.11932.31SE76.75741
14-5.2744827.992517.1262SE82.03651
1560.565157.56329.1937SE105.1841
1645.23443.038415.15205SE40.30371
1763.045443.95532.4871SE26.03821
1823.013337.113243.3749SE48.85781
1963.621344.75292.33662SE48.77471
2067.775793.061826.1981SE71.20351
2141.80834.7022940.0845SE21.86271
2222.249892.61072.50899SE41.75871
2362.352757.055623.2777SE39.84221
2425.291814.579528.8659SE58.10921
2546.27447.233625.0653SE21.15541
2625.5126-0.55827432.7383SE20.98071
2757.212429.677433.6527SE50.07531
2842.52432.1903810.0056SE51.92661
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection
8.88-26.30.38740.403701952
7.09-8.880.3810.392801991
6.21-7.090.41170.422801950
5.65-6.210.38280.390401953
5.25-5.650.36540.372701995
4.94-5.250.35570.363401983
4.69-4.940.36730.373901992
4.49-4.690.34280.349901866
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å26.28 Å
Phasing dmFOM : 0.55 / FOM acentric: 0.55 / FOM centric: 0.45 / Reflection: 39493 / Reflection acentric: 37868 / Reflection centric: 1625
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-26.2850.890.890.517141531183
4.8-7.70.820.830.5252964979317
3.9-4.80.810.820.666396351288
3.4-3.90.70.710.5166876439248
2.9-3.40.390.390.351182811448380
2.7-2.90.160.160.273297120209

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVE2.05phasing
MOLREPphasing
CNS1.1refinement
PHENIXphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB entry 1JQ3

1jq3


Resolution: 2.7→26.29 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.53 / Cross valid method: THROUGHOUT / Details: MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3788 10 %random
Rwork0.188 ---
all-39529 --
obs-37779 95.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 52.816 Å2 / ksol: 0.343792 e/Å3
Displacement parametersBiso max: 139.28 Å2 / Biso mean: 43.83 Å2 / Biso min: 4.12 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å20.35 Å2
2--14.58 Å20 Å2
3----11.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.7→26.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8868 0 0 576 9444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.156
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg23.9
X-RAY DIFFRACTIONx_torsion_impr_deg1.11
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.7-2.820.39146210.10.28441040.0184903456693.1
2.82-2.970.31848710.30.25542230.0144950471095.1
2.97-3.160.29748610.30.22542210.0134906470795.9
3.16-3.40.27148810.30.20242700.0124933475896.4
3.4-3.740.2264589.60.18443080.0114925476696.8
3.74-4.280.2334539.50.16343220.0114934477596.8
4.28-5.390.17351410.80.13442420.0084966475695.8
5.39-26.290.2394409.30.19643010.0115043474194
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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