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

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Basic information

Entry
Database: PDB / ID: 5xnf
TitleCrystal structure of the branched-chain polyamine synthase (BpsA) from Thermococcus kodakarensis
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
: / N(4)-bis(aminopropyl)spermidine synthase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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)85,2326
Polymers84,8922
Non-polymers3404
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-55 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.661, 105.167, 80.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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/T7 tag
Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 100mM NaCl, 100mM lithium sulfate, 100mM ADA (pH6.5), 11.5% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic temperature
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 60904 / % possible obs: 100 % / Redundancy: 14.6 % / Rsym value: 0.109 / Net I/σ(I): 23.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000v706cdata reduction
HKL-2000v706cdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QM3

2qm3


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 12.461 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.15 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2991 4.9 %RANDOM
Rwork0.203 ---
obs0.205 57839 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2.65 Å20 Å2
3---4.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5670 0 17 149 5836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0195819
X-RAY DIFFRACTIONr_bond_other_d0.0050.025535
X-RAY DIFFRACTIONr_angle_refined_deg2.1641.9687889
X-RAY DIFFRACTIONr_angle_other_deg1.2573.00112736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3745700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65223.841289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.311151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2191548
X-RAY DIFFRACTIONr_chiral_restr0.1380.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216499
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021317
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_it2.0542.7772800
X-RAY DIFFRACTIONr_mcbond_other2.0442.7752799
X-RAY DIFFRACTIONr_mcangle_it3.14.1523497
X-RAY DIFFRACTIONr_mcangle_other3.1024.1543498
X-RAY DIFFRACTIONr_scbond_it3.0873.233019
X-RAY DIFFRACTIONr_scbond_other3.0863.233019
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9634.6964392
X-RAY DIFFRACTIONr_long_range_B_refined10.39526.99125158
X-RAY DIFFRACTIONr_long_range_B_other10.41126.93925045
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 250 -
Rwork0.39 4148 -
obs--98.02 %
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)
10.9005-0.0119-0.03810.88680.00490.073-0.0562-0.00410.16730.02690.0554-0.0802-0.05520.0020.00070.1598-0.0081-0.01870.1019-0.00130.039-16.7904-23.2774-20.6907
20.7729-0.01030.03180.9936-0.02710.0722-0.0443-0.0061-0.10480.02340.04940.14420.03630.01-0.00510.1643-0.00850.00670.11850.00780.035-27.7527-49.2703-20.6677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 348
2X-RAY DIFFRACTION2B-1 - 348

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