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

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Basic information

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


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
5'-DEOXY-5'-METHYLTHIOADENOSINE / SPERMIDINE / Polyamine aminopropyltransferase
Similarity search - Component
Biological speciesPyrobaculum calidifontis JCM 11548 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyamine aminopropyltransferase
B: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6056
Polymers69,7202
Non-polymers8854
Water9,980554
1
A: Polyamine aminopropyltransferase
B: Polyamine aminopropyltransferase
hetero molecules

A: Polyamine aminopropyltransferase
B: Polyamine aminopropyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,20912
Polymers139,4394
Non-polymers1,7708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16530 Å2
ΔGint-48 kcal/mol
Surface area36930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.567, 57.256, 54.485
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34859.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis JCM 11548 (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.: 2 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium acetate, PEG 2000MME

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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: Jul 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→43.1 Å / Num. obs: 166200 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 8259 / CC1/2: 0.778

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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: 1.2→39.23 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.627 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15353 8178 4.9 %RANDOM
Rwork0.11896 ---
obs0.12066 158009 99.12 %-
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: 21.381 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20.29 Å2
2---0.67 Å20 Å2
3---0.87 Å2
Refinement stepCycle: 1 / Resolution: 1.2→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 60 554 5195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0134856
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174592
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.6616609
X-RAY DIFFRACTIONr_angle_other_deg1.5951.58610613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5685597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12121.119268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37815814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9111541
X-RAY DIFFRACTIONr_chiral_restr0.1140.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025445
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021060
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_it2.1131.8792340
X-RAY DIFFRACTIONr_mcbond_other2.1141.8792339
X-RAY DIFFRACTIONr_mcangle_it2.3812.832935
X-RAY DIFFRACTIONr_mcangle_other2.3812.8312936
X-RAY DIFFRACTIONr_scbond_it4.6112.3042516
X-RAY DIFFRACTIONr_scbond_other4.612.3042517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9193.2933669
X-RAY DIFFRACTIONr_long_range_B_refined4.77823.6745358
X-RAY DIFFRACTIONr_long_range_B_other4.51522.9875245
X-RAY DIFFRACTIONr_rigid_bond_restr5.16939448
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 582 -
Rwork0.261 11724 -
obs--99.72 %

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