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- PDB-5xnh: Crystal structure of the branched-chain polyamine synthase (BpsA)... -

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Basic information

Entry
Database: PDB / ID: 5xnh
TitleCrystal structure of the branched-chain polyamine synthase (BpsA) in complex with spermidine
ComponentsN(4)-bis(aminopropyl)spermidine synthase
KeywordsTRANSFERASE / Polyamine biosynthesis / N(4)-bis(aminopropyl)spermidine synthase
Function / homology
Function and homology information


N4-bis(aminopropyl)spermidine synthase / rRNA (adenine-N6-)-methyltransferase activity / polyamine biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / transferase activity / cytoplasm
Similarity search - Function
N(4)-bis(aminopropyl)spermidine synthase, C-terminal / N(4)-bis(aminopropyl)spermidine synthase / Branched-chain polyamine synthase A C-terminal domain / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle ...N(4)-bis(aminopropyl)spermidine synthase, C-terminal / N(4)-bis(aminopropyl)spermidine synthase / Branched-chain polyamine synthase A C-terminal domain / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / SPERMIDINE / N(4)-bis(aminopropyl)spermidine synthase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsMizohata, E. / Tse, K.M. / Fujita, J. / Inoue, T.
CitationJournal: FEBS J. / Year: 2017
Title: Active site geometry of a novel aminopropyltransferase for biosynthesis of hyperthermophile-specific branched-chain polyamine.
Authors: Hidese, R. / Tse, K.M. / Kimura, S. / Mizohata, E. / Fujita, J. / Horai, Y. / Umezawa, N. / Higuchi, T. / Niitsu, M. / Oshima, T. / Imanaka, T. / Inoue, T. / Fujiwara, S.
History
DepositionMay 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N(4)-bis(aminopropyl)spermidine synthase
H: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2385
Polymers84,8922
Non-polymers3463
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-9 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.869, 78.783, 79.407
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N(4)-bis(aminopropyl)spermidine synthase / Branched-chain polyamine synthase A


Mass: 42445.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: bpsA, TK1691 / Plasmid: pET28a
Details (production host): N-terminal HisTag/thrombin digestion site
Production host: Escherichia coli (E. coli) / Strain (production host): BL-21CodonPlus(DE3)RIL
References: UniProt: Q5JIZ3, N4-bis(aminopropyl)spermidine synthase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIn chain A, residue numbers 344, 345 are simply skipped. In chain H, residue numbers 345-347 are ...In chain A, residue numbers 344, 345 are simply skipped. In chain H, residue numbers 345-347 are simply skipped.

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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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Sodium chloride, 0.1M Tris pH 8.5, 12 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→50.01 Å / Num. obs: 47518 / % possible obs: 99.9 % / Redundancy: 5.6 % / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 1.95→50.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.439 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22493 1964 4.9 %RANDOM
Rwork0.17122 ---
obs0.17391 38437 84.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.426 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å2-0 Å20.24 Å2
2---0.53 Å20 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.95→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 21 164 5663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195615
X-RAY DIFFRACTIONr_bond_other_d0.0020.025379
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9647600
X-RAY DIFFRACTIONr_angle_other_deg1.094312372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6755674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01223.636275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46715980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5831548
X-RAY DIFFRACTIONr_chiral_restr0.1110.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216258
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021286
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_it2.0312.2922708
X-RAY DIFFRACTIONr_mcbond_other2.0292.2922707
X-RAY DIFFRACTIONr_mcangle_it2.9983.4193375
X-RAY DIFFRACTIONr_mcangle_other2.9983.423376
X-RAY DIFFRACTIONr_scbond_it2.9622.7542907
X-RAY DIFFRACTIONr_scbond_other2.9612.7542908
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7763.9774225
X-RAY DIFFRACTIONr_long_range_B_refined7.20344.03323823
X-RAY DIFFRACTIONr_long_range_B_other7.19844.04123728
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 108 -
Rwork0.202 1530 -
obs--46.92 %

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