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- PDB-7xii: Crystal structure of the aminopropyltransferase, SpeE from hypert... -

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Basic information

Entry
Database: PDB / ID: 7xii
TitleCrystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) & aminopropylagmatine
ComponentsPolyamine aminopropyltransferase
KeywordsTRANSFERASE / POLYAMINE BIOSYNTHESIS
Function / homology
Function and homology information


thermospermine synthase activity / spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytoplasm
Similarity search - Function
Polyamine biosynthesis domain, conserved site / Polyamine biosynthesis (PABS) domain signature. / Spermidine/spermine synthases / Polyamine biosynthesis domain / Spermidine synthase, tetramerisation domain / Spermidine synthase, tetramerisation domain superfamily / Spermidine synthase tetramerisation domain / Polyamine biosynthesis (PABS) domain profile. / Spermine/spermidine synthase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
1-{4-[(3-aminopropyl)amino]butyl}guanidine / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesPyrobaculum calidifontis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMizohata, E. / Yasuda, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJPR17GB Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)19H05780 Japan
New Energy and Industrial Technology Development Organization (NEDO)JPNP18016 Japan
CitationJournal: Catalysts / Year: 2022
Title: Substrate Specificity of an Aminopropyltransferase and the Biosynthesis Pathway of Polyamines in the Hyperthermophilic Crenarchaeon Pyrobaculum calidifontis.
Authors: Fukuda, W. / Osaki, M. / Yasuda, Y. / Hidese, R. / Higuchi, T. / Umezawa, N. / Fujiwara, S. / Mizohata, E.
History
DepositionApr 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: Polyamine aminopropyltransferase
B: Polyamine aminopropyltransferase
C: Polyamine aminopropyltransferase
D: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,61613
Polymers139,4394
Non-polymers2,1779
Water9,782543
1
A: Polyamine aminopropyltransferase
B: Polyamine aminopropyltransferase
hetero molecules

C: Polyamine aminopropyltransferase
D: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,61613
Polymers139,4394
Non-polymers2,1779
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area12050 Å2
ΔGint-73 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.163, 57.173, 97.308
Angle α, β, γ (deg.)77.19, 78.32, 88.49
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEUAA4 - 28824 - 308
21VALVALLEULEUBB4 - 28824 - 308
12VALVALARGARGAA4 - 28924 - 309
22VALVALARGARGCC4 - 28924 - 309
13VALVALLEULEUAA4 - 28824 - 308
23VALVALLEULEUDD4 - 28824 - 308
14VALVALLEULEUBB4 - 28824 - 308
24VALVALLEULEUCC4 - 28824 - 308
15ARGARGARGARGBB2 - 28922 - 309
25ARGARGARGARGDD2 - 28922 - 309
16VALVALLEULEUCC4 - 28824 - 308
26VALVALLEULEUDD4 - 28824 - 308

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Polyamine aminopropyltransferase / Putrescine aminopropyltransferase / PAPT / Spermidine synthase / SPDS / SPDSY


Mass: 34859.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis (archaea) / Strain: DSM 21063 / JCM 11548 / VA1 / Gene: speE, Pcal_0772 / Production host: Escherichia coli (E. coli) / References: UniProt: A3MU81, spermidine synthase
#2: Chemical
ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE


Mass: 297.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AG3 / 1-{4-[(3-aminopropyl)amino]butyl}guanidine / N1-aminopropylagmatine


Mass: 187.286 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H21N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium formate, HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.25→46.47 Å / Num. obs: 53669 / % possible obs: 99.5 % / Redundancy: 9.9 % / CC1/2: 0.995 / Net I/σ(I): 13.3
Reflection shellResolution: 2.25→2.32 Å / Num. unique obs: 4661 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XIF

7xif


Resolution: 2.25→46.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.416 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17021 2616 4.9 %RANDOM
Rwork0.14918 ---
obs0.15023 51035 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.403 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0.33 Å2-0.33 Å2
2--0.26 Å20.22 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 2.25→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9144 0 147 543 9834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0129507
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.65412910
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4151144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93121.484512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.942151566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.351570
X-RAY DIFFRACTIONr_chiral_restr0.1110.21235
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027304
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.2012.1454592
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0573.2055728
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1482.5474915
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.27329.94114516
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A94770.06
12B94770.06
21A95510.05
22C95510.05
31A95290.06
32D95290.06
41B95130.06
42C95130.06
51B96450.06
52D96450.06
61C95520.06
62D95520.06
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 152 -
Rwork0.165 3850 -
obs--99.85 %

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