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- PDB-6j27: Crystal structure of the branched-chain polyamine synthase from T... -

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Basic information

Entry
Database: PDB / ID: 6j27
TitleCrystal structure of the branched-chain polyamine synthase from Thermus thermophilus (Tth-BpsA) in complex with N4-aminopropylspermidine 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 / metal ion binding / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 5'-DEOXY-5'-METHYLTHIOADENOSINE / N,N-bis(3-aminopropyl)butane-1,4-diamine / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N(4)-bis(aminopropyl)spermidine synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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
C: N(4)-bis(aminopropyl)spermidine synthase
D: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,09326
Polymers166,5774
Non-polymers3,51622
Water12,394688
1
A: N(4)-bis(aminopropyl)spermidine synthase
B: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,17514
Polymers83,2892
Non-polymers1,88612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint1 kcal/mol
Surface area24170 Å2
MethodPISA
2
C: N(4)-bis(aminopropyl)spermidine synthase
D: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,91812
Polymers83,2892
Non-polymers1,63010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-2 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.570, 158.606, 71.936
Angle α, β, γ (deg.)90.00, 118.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 41644.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: bpsA, TT_C0171 / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)
References: UniProt: Q72L89, N4-bis(aminopropyl)spermidine synthase

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Non-polymers , 6 types, 710 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N5O3S
#4: Chemical
ChemComp-N4P / N,N-bis(3-aminopropyl)butane-1,4-diamine / N4-aminopropylspermidine


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir: 0.04 M sodium chloride , 0.04 M Tris pH 8.0, 27%(v/v) PEG 350MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. obs: 156847 / % possible obs: 99.3 % / Redundancy: 5.3 % / Net I/σ(I): 15.1
Reflection shellResolution: 1.66→1.71 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q3M

2q3m


Resolution: 1.66→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.75 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20618 7822 5 %RANDOM
Rwork0.16724 ---
obs0.16918 148976 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-0.44 Å2
2--3.28 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: 1 / Resolution: 1.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10885 0 231 688 11804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911575
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211237
X-RAY DIFFRACTIONr_angle_refined_deg1.921.98515738
X-RAY DIFFRACTIONr_angle_other_deg1.0993.00125705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78251417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3222.248565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.133151832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.42515149
X-RAY DIFFRACTIONr_chiral_restr0.1190.21693
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113011
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022734
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_it2.1652.4955554
X-RAY DIFFRACTIONr_mcbond_other2.1652.4955553
X-RAY DIFFRACTIONr_mcangle_it2.9423.7336952
X-RAY DIFFRACTIONr_mcangle_other2.9423.7336953
X-RAY DIFFRACTIONr_scbond_it3.4222.9586021
X-RAY DIFFRACTIONr_scbond_other3.4212.9586021
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2194.2598768
X-RAY DIFFRACTIONr_long_range_B_refined6.45524.38749085
X-RAY DIFFRACTIONr_long_range_B_other6.43624.30748659
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.664→1.707 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 526 -
Rwork0.276 10047 -
obs--89.78 %

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