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

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Basic information

Entry
Database: PDB / ID: 5xnc
TitleCrystal structure of the branched-chain polyamine synthase (BpsA) in complex with N4-aminopropylspermidine and 5-methylthioadenosine
ComponentsN(4)-bis(aminopropyl)spermidine synthase
KeywordsTRANSFERASE / Polyamine biosynthesis / spermidine / N4-aminopropylspermidine / 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 / 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
: / 5'-DEOXY-5'-METHYLTHIOADENOSINE / N,N-bis(3-aminopropyl)butane-1,4-diamine / DI(HYDROXYETHYL)ETHER / N(4)-bis(aminopropyl)spermidine synthase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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 1.1Mar 27, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
E: N(4)-bis(aminopropyl)spermidine synthase
F: N(4)-bis(aminopropyl)spermidine synthase
G: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,70235
Polymers297,1227
Non-polymers4,58028
Water19,1141061
1
A: N(4)-bis(aminopropyl)spermidine synthase
B: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,42212
Polymers84,8922
Non-polymers1,53010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: N(4)-bis(aminopropyl)spermidine synthase
D: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,16310
Polymers84,8922
Non-polymers1,2718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: N(4)-bis(aminopropyl)spermidine synthase
F: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1159
Polymers84,8922
Non-polymers1,2237
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules

G: N(4)-bis(aminopropyl)spermidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0038
Polymers84,8922
Non-polymers1,1116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)137.533, 50.978, 402.428
Angle α, β, γ (deg.)90.00, 93.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-403-

FE

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 10 - 340 / Label seq-ID: 30 - 360

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.351342, 0.935615, 0.0344), (0.93524, 0.349023, 0.059245), (0.043424, 0.052987, -0.997651)27.59015, -21.62372, 58.63358
3given(-0.068101, -0.429044, 0.900713), (-0.408378, -0.811723, -0.417532), (0.910269, -0.396266, -0.119932)-48.3593, 66.47154, -2.10757
4given(-0.339123, -0.613862, -0.71286), (-0.177507, -0.702398, 0.689296), (-0.923844, 0.360294, 0.129234)107.43772, -42.56391, 62.14824
5given(0.827398, 0.475036, -0.299588), (-0.554392, 0.776126, -0.300463), (0.089788, 0.414692, 0.905521)48.21684, 25.35276, -114.92907
6given(-0.811732, 0.566295, -0.142831), (0.577121, 0.740267, -0.34487), (-0.089565, -0.362373, -0.92772)30.39639, 27.52511, 176.39474
7given(0.148706, -0.571199, 0.807229), (-0.1208, -0.820684, -0.558467), (0.981475, -0.014466, -0.191041)-127.96062, 149.4792, 14.003

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Components

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Protein , 1 types, 7 molecules ABCDEFG

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


Mass: 42445.941 Da / Num. of mol.: 7
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

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Non-polymers , 7 types, 1089 molecules

#2: Chemical
ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C11H15N5O3S
#3: Chemical
ChemComp-N4P / N,N-bis(3-aminopropyl)butane-1,4-diamine / N4-aminopropylspermidine


Mass: 202.340 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H26N4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1061 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM sodium citrate tribasic dihydrate (pH 5.6), 2.5 M (w/v) 1,6-hexanediol
Temp details: 4 degree C

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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: Jun 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 241983 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rsym value: 0.061 / Net I/σ(I): 27.7
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000v706cdata reduction
HKL-2000v706cdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→43.53 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.167 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 12128 5 %RANDOM
Rwork0.161 ---
obs0.164 229853 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20.04 Å2
2--0.27 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19991 0 298 1061 21350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.01920747
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219779
X-RAY DIFFRACTIONr_angle_refined_deg2.2831.97928113
X-RAY DIFFRACTIONr_angle_other_deg1.2673.00145503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73352475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86323.851013
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48153571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.61715168
X-RAY DIFFRACTIONr_chiral_restr0.170.23146
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02123036
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024675
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_it1.9452.4459891
X-RAY DIFFRACTIONr_mcbond_other1.9442.4459890
X-RAY DIFFRACTIONr_mcangle_it2.7123.65412354
X-RAY DIFFRACTIONr_mcangle_other2.7123.65412355
X-RAY DIFFRACTIONr_scbond_it3.0292.81810855
X-RAY DIFFRACTIONr_scbond_other3.0282.81810855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7184.09115755
X-RAY DIFFRACTIONr_long_range_B_refined6.59423.71792155
X-RAY DIFFRACTIONr_long_range_B_other6.5723.57691455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1944medium positional0.150.5
2B1944medium positional0.170.5
3C1944medium positional0.150.5
4D1944medium positional0.140.5
5E1944medium positional0.150.5
6F1944medium positional0.210.5
7G1944medium positional0.230.5
1A3281loose positional0.635
2B3281loose positional0.655
3C3281loose positional0.635
4D3281loose positional0.585
5E3281loose positional0.75
6F3281loose positional0.785
7G3281loose positional0.725
1A1944medium thermal9.442
2B1944medium thermal9.042
3C1944medium thermal6.132
4D1944medium thermal5.492
5E1944medium thermal6.792
6F1944medium thermal7.632
7G1944medium thermal15.932
1A3281loose thermal9.6610
2B3281loose thermal9.0610
3C3281loose thermal7.1210
4D3281loose thermal6.3110
5E3281loose thermal7.1510
6F3281loose thermal8.3310
7G3281loose thermal15.7810
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 861 -
Rwork0.297 16804 -
obs--99.08 %
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)
10.3487-0.2642-0.31750.41420.42461.1596-0.00650.02120.0365-0.14520.0122-0.0749-0.0738-0.1502-0.00570.1736-0.0010.01940.0552-0.00480.210619.44531.951315.5801
20.6644-0.4686-0.41290.62540.42931.0496-0.1137-0.12070.010.1080.1236-0.03530.1540.0546-0.00990.12060.0657-0.0210.0685-0.02770.213623.0242-1.631744.083
30.2901-0.0596-0.07410.28680.26481.7648-0.0231-0.10920.0517-0.0736-0.02630.0482-0.2132-0.27630.04940.09940.1461-0.05260.2523-0.08440.209137.81116.236985.8334
40.328-0.073-0.25010.27830.34321.8789-0.0044-0.08940.0025-0.0372-0.0013-0.0604-0.01650.22090.00570.06620.1104-0.03590.2276-0.04760.198864.98325.923687.3751
50.49730.0525-0.35330.57970.12711.8785-0.00390.0707-0.06480.07710.04710.03440.1947-0.1372-0.04330.08430.0941-0.00520.2022-0.01780.11280.820922.3232133.8257
60.6942-0.0255-0.38230.45120.31351.83730.0384-0.02050.0040.35230.0894-0.0183-0.11470.1978-0.12780.39820.1194-0.00270.178-0.03960.07728.542733.1556159.5901
70.6989-0.1154-0.74160.44680.10251.4759-0.02220.2145-0.0873-0.0123-0.09510.12380.3334-0.41540.11720.3202-0.1159-0.0150.1713-0.04640.070841.279436.8151201.0393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 351
2X-RAY DIFFRACTION2B-2 - 351
3X-RAY DIFFRACTION3C-1 - 351
4X-RAY DIFFRACTION4D-1 - 351
5X-RAY DIFFRACTION5E-1 - 351
6X-RAY DIFFRACTION6F-1 - 351
7X-RAY DIFFRACTION7G-1 - 351

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