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- PDB-3o4f: Crystal Structure of Spermidine Synthase from E. coli -

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Basic information

Entry
Database: PDB / ID: 3o4f
TitleCrystal Structure of Spermidine Synthase from E. coli
ComponentsSpermidine synthase
KeywordsTRANSFERASE / AMINOPROPYLTRANSFERASE / POLYAMINE SYNTHASE / ROSSMANN FOLD / POLYAMINE BIOSYNTHESIS / SPERMIDINE BIOSYNTHESIS
Function / homology
Function and homology information


thermospermine synthase / spermine synthase / spermine synthase activity / cadaverine aminopropyltransferase activity / thermospermine synthase activity / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / cytosol
Similarity search - Function
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, 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
Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhou, X. / Tkaczuk, K.L. / Chruszcz, M. / Chua, T.K. / Minor, W. / Sivaraman, J.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket
Authors: Zhou, X. / Chua, T.K. / Tkaczuk, K.L. / Bujnicki, J.M. / Sivaraman, J.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 18, 2010ID: 3ADN
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spermidine synthase
B: Spermidine synthase
C: Spermidine synthase
D: Spermidine synthase
E: Spermidine synthase
F: Spermidine synthase
G: Spermidine synthase
H: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,46039
Polymers265,4828
Non-polymers2,97831
Water23413
1
A: Spermidine synthase
B: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9478
Polymers66,3702
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-24 kcal/mol
Surface area22170 Å2
MethodPISA
2
C: Spermidine synthase
D: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,33112
Polymers66,3702
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-23 kcal/mol
Surface area22200 Å2
MethodPISA
3
E: Spermidine synthase
F: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,13910
Polymers66,3702
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-24 kcal/mol
Surface area22130 Å2
MethodPISA
4
G: Spermidine synthase
H: Spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0439
Polymers66,3702
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-22 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.110, 123.110, 210.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

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Components

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


Mass: 33185.215 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: SPEE / Plasmid: PCA24N / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09158, spermidine synthase
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M LiSO4, 0.1M Na Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 69092 / % possible obs: 95.3 % / Redundancy: 10.6 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.037 / Net I/σ(I): 20.975
Reflection shellResolution: 2.85→2.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.391 / Num. unique all: 6394 / Χ2: 0.426 / % possible all: 94.7

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Processing

SoftwareName: REFMAC / Version: 5.6.0070 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1INL

1inl


Resolution: 2.9→48.294 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.913 / SU B: 36.465 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 3429 5 %RANDOM
Rwork0.20812 ---
obs0.20975 64857 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.813 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17351 0 155 13 17519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02117927
X-RAY DIFFRACTIONr_bond_other_d00.0211423
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.92624379
X-RAY DIFFRACTIONr_angle_other_deg4.21327718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12452191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05924.227925
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.339152675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7831579
X-RAY DIFFRACTIONr_chiral_restr0.1110.22626
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220349
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023870
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3239 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.160.05
Btight positional0.190.05
Ctight positional0.190.05
Dtight positional0.160.05
Etight positional0.230.05
Ftight positional0.120.05
Gtight positional0.370.05
Htight positional0.180.05
Atight thermal8.90.5
Btight thermal8.540.5
Ctight thermal9.930.5
Dtight thermal8.070.5
Etight thermal8.690.5
Ftight thermal10.40.5
Gtight thermal11.950.5
Htight thermal10.870.5
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 213 -
Rwork0.341 4263 -
obs--88.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6473-0.8841-0.12572.65420.18252.7034-0.3688-0.17670.64720.22780.2075-0.4318-0.58290.85650.16120.3286-0.1387-0.310.3951-0.13180.516377.6393-35.903839.2055
21.4211-0.3098-0.23213.0518-0.37212.1508-0.2323-0.1010.38430.04180.10750.5807-0.1809-0.4960.12470.14880.1203-0.17710.1632-0.12310.36847.0353-43.542432.4779
32.3454-0.88020.09922.18130.24471.71090.17650.3590.3787-0.2194-0.4172-0.6957-0.60570.55610.24070.3156-0.08170.05990.50550.39960.420727.077215.8008-2.668
42.9868-0.80470.08442.0603-0.19691.98230.10890.3403-0.4717-0.2162-0.2596-0.21360.45190.22110.15070.19820.14380.10060.19080.08620.22518.3677-14.85282.8827
53.4618-0.92260.44191.29950.34042.3564-0.29540.62750.9528-0.36120.0463-0.611-0.70930.77910.24910.424-0.40710.02930.59420.26040.535380.1829-38.4389-1.8323
63.8794-0.13311.21412.22350.95692.49010.30580.373-0.51380.08010.1221-0.42730.60790.9118-0.4280.18870.2172-0.04970.4724-0.10280.199581.4702-69.76985.6799
71.0285-0.4841-0.41564.1732-0.44982.59360.1249-0.21890.27340.7178-0.3406-0.7053-0.77810.61420.21580.5845-0.411-0.24930.3090.12690.225424.839216.681138.4152
81.98621.1273-0.5734.1902-1.6022.59670.29160.20230.63030.93870.20821.2367-1.1053-0.6442-0.49980.54390.27050.27690.18390.08440.4196-6.282520.303331.281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 280
2X-RAY DIFFRACTION2B5 - 280
3X-RAY DIFFRACTION3C5 - 280
4X-RAY DIFFRACTION4D5 - 280
5X-RAY DIFFRACTION5E5 - 280
6X-RAY DIFFRACTION6F5 - 280
7X-RAY DIFFRACTION7G5 - 280
8X-RAY DIFFRACTION8H5 - 280

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