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- PDB-6j26: Crystal structure of the branched-chain polyamine synthase from T... -

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Basic information

Entry
Database: PDB / ID: 6j26
TitleCrystal structure of the branched-chain polyamine synthase from Thermococcus kodakarensis (Tk-BpsA) in complex with N4-bis(aminopropyl)spermidine and 5'-methylthioadenosine
ComponentsN(4)-bis(aminopropyl)spermidine synthase
KeywordsTRANSFERASE / N(4)-bis(aminopropyl)spermidine synthase / POLYAMINE BIOSYNTHESIS / SPERMIDINE / BRANCHED POLYAMINES
Function / homology
Function and homology information


N4-bis(aminopropyl)spermidine synthase / 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 ...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
Chem-B5L / : / 5'-DEOXY-5'-METHYLTHIOADENOSINE / N(4)-bis(aminopropyl)spermidine synthase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMizohata, E. / Toyoda, M. / Fujita, J. / Inoue, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR17GB Japan
CitationJournal: Febs J. / Year: 2019
Title: The C-terminal flexible region of branched-chain polyamine synthase facilitates substrate specificity and catalysis.
Authors: Hidese, R. / Toyoda, M. / Yoshino, K.I. / Fukuda, W. / Wihardja, G.A. / Kimura, S. / Fujita, J. / Niitsu, M. / Oshima, T. / Imanaka, T. / Mizohata, E. / Fujiwara, S.
History
DepositionDec 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
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
B: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0717
Polymers84,8922
Non-polymers1,1795
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-26 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.170, 74.170, 105.934
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21CODONPLUS(DE3)RIL
References: UniProt: Q5JIZ3, N4-bis(aminopropyl)spermidine synthase
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Chemical ChemComp-B5L / N~1~,N~1~,N~1~-tris(3-azaniumylpropyl)butane-1,4-diaminium / N4-bis(aminopropyl)spermidine


Mass: 264.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H38N5
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Reservoir: 0.015 M tricine pH 8.5, 24%(v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 44104 / % possible obs: 100 % / Redundancy: 10.1 % / Net I/σ(I): 26.1
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XNC

5xnc


Resolution: 2→40.87 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.506 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22769 2182 5 %RANDOM
Rwork0.19603 ---
obs0.19753 41889 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.088 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0 Å2
2--0.01 Å20 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5712 0 77 204 5993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195938
X-RAY DIFFRACTIONr_bond_other_d0.0010.025667
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9788058
X-RAY DIFFRACTIONr_angle_other_deg0.873313044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65923.836292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.321549
X-RAY DIFFRACTIONr_chiral_restr0.0560.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216611
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021344
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_it0.5363.1912830
X-RAY DIFFRACTIONr_mcbond_other0.5363.1912829
X-RAY DIFFRACTIONr_mcangle_it0.9424.7833536
X-RAY DIFFRACTIONr_mcangle_other0.9414.7833537
X-RAY DIFFRACTIONr_scbond_it0.5723.2723108
X-RAY DIFFRACTIONr_scbond_other0.5723.2723109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9994.8754519
X-RAY DIFFRACTIONr_long_range_B_refined2.16237.3126806
X-RAY DIFFRACTIONr_long_range_B_other2.07737.1536748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 196 -
Rwork0.257 3055 -
obs--99.21 %

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