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

ID or keywords:

Entry

Database: PDB / ID: 7xig

Title

Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) and spermine

Components

Polyamine aminopropyltransferase

Keywords

TRANSFERASE / POLYAMINE BIOSYNTHESIS

Function / homology

Function and homology information

spermidine synthase / spermidine synthase activity / spermidine biosynthetic process / cytoplasm
Similarity search - Function

Biological species

Pyrobaculum calidifontis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Mizohata, E. / Yasuda, Y.

Funding support

Japan, 3items

Organization	Grant number	Country
Japan Science and Technology	JPMJPR17GB	Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)	19H05780	Japan
New Energy and Industrial Technology Development Organization (NEDO)	JPNP18016	Japan

Citation

Journal: 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

Deposition	Apr 13, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 15, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7xig.cif.gz	478 KB	Display	PDBx/mmCIF format
PDB format	pdb7xig.ent.gz	389.5 KB	Display	PDB format
PDBx/mmJSON format	7xig.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xi/7xig ftp://data.pdbj.org/pub/pdb/validation_reports/xi/7xig	HTTPS FTP

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Related structure data

Related structure data	7xifSC 7xihC 7xiiC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#15 - Mar 2001 Transfer RNA similarity (1) #23 - Nov 2001 DNA similarity (1)

Deposited unit

A: Polyamine aminopropyltransferase

B: Polyamine aminopropyltransferase

C: Polyamine aminopropyltransferase

D: Polyamine aminopropyltransferase

E: Polyamine aminopropyltransferase

F: Polyamine aminopropyltransferase

G: Polyamine aminopropyltransferase

H: Polyamine aminopropyltransferase

hetero molecules

283 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Polyamine aminopropyltransferase

B: Polyamine aminopropyltransferase

hetero molecules

C: Polyamine aminopropyltransferase

D: Polyamine aminopropyltransferase

hetero molecules

defined by author&software
142 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Polyamine aminopropyltransferase

F: Polyamine aminopropyltransferase

hetero molecules

G: Polyamine aminopropyltransferase

H: Polyamine aminopropyltransferase

hetero molecules

defined by author&software
142 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.828, 80.392, 97.844
Angle α, β, γ (deg.)	72.46, 89.13, 88.08
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	VAL	LEU	LEU	A	A	4 - 288	24 - 308
2	1	VAL	VAL	LEU	LEU	B	B	4 - 288	24 - 308
1	2	VAL	VAL	ARG	ARG	A	A	4 - 289	24 - 309
2	2	VAL	VAL	ARG	ARG	C	C	4 - 289	24 - 309
1	3	VAL	VAL	LEU	LEU	A	A	4 - 288	24 - 308
2	3	VAL	VAL	LEU	LEU	D	D	4 - 288	24 - 308
1	4	VAL	VAL	ARG	ARG	A	A	4 - 289	24 - 309
2	4	VAL	VAL	ARG	ARG	E	E	4 - 289	24 - 309
1	5	VAL	VAL	ARG	ARG	A	A	4 - 289	24 - 309
2	5	VAL	VAL	ARG	ARG	F	F	4 - 289	24 - 309
1	6	VAL	VAL	ARG	ARG	A	A	4 - 289	24 - 309
2	6	VAL	VAL	ARG	ARG	G	G	4 - 289	24 - 309
1	7	VAL	VAL	LEU	LEU	A	A	4 - 288	24 - 308
2	7	VAL	VAL	LEU	LEU	H	H	4 - 288	24 - 308
1	8	VAL	VAL	LEU	LEU	B	B	4 - 288	24 - 308
2	8	VAL	VAL	LEU	LEU	C	C	4 - 288	24 - 308
1	9	ARG	ARG	ARG	ARG	B	B	2 - 289	22 - 309
2	9	ARG	ARG	ARG	ARG	D	D	2 - 289	22 - 309
1	10	VAL	VAL	LEU	LEU	B	B	4 - 288	24 - 308
2	10	VAL	VAL	LEU	LEU	E	E	4 - 288	24 - 308
1	11	VAL	VAL	LEU	LEU	B	B	4 - 288	24 - 308
2	11	VAL	VAL	LEU	LEU	F	F	4 - 288	24 - 308
1	12	VAL	VAL	LEU	LEU	B	B	4 - 288	24 - 308
2	12	VAL	VAL	LEU	LEU	G	G	4 - 288	24 - 308
1	13	ARG	ARG	ARG	ARG	B	B	2 - 289	22 - 309
2	13	ARG	ARG	ARG	ARG	H	H	2 - 289	22 - 309
1	14	VAL	VAL	LEU	LEU	C	C	4 - 288	24 - 308
2	14	VAL	VAL	LEU	LEU	D	D	4 - 288	24 - 308
1	15	VAL	VAL	ARG	ARG	C	C	4 - 289	24 - 309
2	15	VAL	VAL	ARG	ARG	E	E	4 - 289	24 - 309
1	16	VAL	VAL	ARG	ARG	C	C	4 - 289	24 - 309
2	16	VAL	VAL	ARG	ARG	F	F	4 - 289	24 - 309
1	17	VAL	VAL	ARG	ARG	C	C	4 - 289	24 - 309
2	17	VAL	VAL	ARG	ARG	G	G	4 - 289	24 - 309
1	18	VAL	VAL	LEU	LEU	C	C	4 - 288	24 - 308
2	18	VAL	VAL	LEU	LEU	H	H	4 - 288	24 - 308
1	19	VAL	VAL	LEU	LEU	D	D	4 - 288	24 - 308
2	19	VAL	VAL	LEU	LEU	E	E	4 - 288	24 - 308
1	20	VAL	VAL	LEU	LEU	D	D	4 - 288	24 - 308
2	20	VAL	VAL	LEU	LEU	F	F	4 - 288	24 - 308
1	21	VAL	VAL	LEU	LEU	D	D	4 - 288	24 - 308
2	21	VAL	VAL	LEU	LEU	G	G	4 - 288	24 - 308
1	22	ARG	ARG	ARG	ARG	D	D	2 - 289	22 - 309
2	22	ARG	ARG	ARG	ARG	H	H	2 - 289	22 - 309
1	23	VAL	VAL	ARG	ARG	E	E	4 - 289	24 - 309
2	23	VAL	VAL	ARG	ARG	F	F	4 - 289	24 - 309
1	24	VAL	VAL	ARG	ARG	E	E	4 - 289	24 - 309
2	24	VAL	VAL	ARG	ARG	G	G	4 - 289	24 - 309
1	25	VAL	VAL	LEU	LEU	E	E	4 - 288	24 - 308
2	25	VAL	VAL	LEU	LEU	H	H	4 - 288	24 - 308
1	26	VAL	VAL	ARG	ARG	F	F	4 - 289	24 - 309
2	26	VAL	VAL	ARG	ARG	G	G	4 - 289	24 - 309
1	27	VAL	VAL	LEU	LEU	F	F	4 - 288	24 - 308
2	27	VAL	VAL	LEU	LEU	H	H	4 - 288	24 - 308
1	28	VAL	VAL	LEU	LEU	G	G	4 - 288	24 - 308
2	28	VAL	VAL	LEU	LEU	H	H	4 - 288	24 - 308

NCS ensembles :

#1: Protein	Polyamine aminopropyltransferase / Putrescine aminopropyltransferase / PAPT / Spermidine synthase / SPDS / SPDSY Mass: 34859.758 Da / Num. of mol.: 8 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.: 8 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SPM / SPERMINE Mass: 202.340 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₂₆N₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / 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.: 765 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium formate, HEPES, PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.25→46.65 Å / Num. obs: 106737 / % possible obs: 99.5 % / Redundancy: 3.6 % / CC_1/2: 0.989 / Net I/σ(I): 5.4
Reflection shell	Resolution: 2.25→2.29 Å / Num. unique obs: 5243 / CC_1/2: 0.813

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Coot		model building
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7XIF

7xif

Resolution: 2.25→46.69 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.946 / SU B: 6.579 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.361 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20743	5275	5 %	RANDOM
R_work	0.17272	-	-	-
obs	0.17442	100802	98.87 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 47.308 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.58 Å²	-0.29 Å²	0.4 Å²
2-	-	-0.7 Å²	-0.94 Å²
3-	-	-	-0.41 Å²

Refinement step

Cycle: 1 / Resolution: 2.25→46.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18268	0	302	765	19335

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	19011
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.467	1.654	25808
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.368	5	2288
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.48	21.575	1016
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.899	15	3128
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.72	15	140
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	2469
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	14572
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.861	4.38	9170
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	5.246	6.558	11449
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	5.963	4.897	9841
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	10.175	60.501	28483
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	9453	0.05
1	2	B	9453	0.05
2	1	A	9464	0.05
2	2	C	9464	0.05
3	1	A	9475	0.05
3	2	D	9475	0.05
4	1	A	9453	0.05
4	2	E	9453	0.05
5	1	A	9530	0.05
5	2	F	9530	0.05
6	1	A	9584	0.04
6	2	G	9584	0.04
7	1	A	9447	0.05
7	2	H	9447	0.05
8	1	B	9479	0.05
8	2	C	9479	0.05
9	1	B	9590	0.05
9	2	D	9590	0.05
10	1	B	9503	0.04
10	2	E	9503	0.04
11	1	B	9515	0.04
11	2	F	9515	0.04
12	1	B	9474	0.05
12	2	G	9474	0.05
13	1	B	9591	0.04
13	2	H	9591	0.04
14	1	C	9458	0.06
14	2	D	9458	0.06
15	1	C	9508	0.04
15	2	E	9508	0.04
16	1	C	9502	0.05
16	2	F	9502	0.05
17	1	C	9484	0.05
17	2	G	9484	0.05
18	1	C	9470	0.05
18	2	H	9470	0.05
19	1	D	9460	0.05
19	2	E	9460	0.05
20	1	D	9533	0.04
20	2	F	9533	0.04
21	1	D	9518	0.05
21	2	G	9518	0.05
22	1	D	9576	0.05
22	2	H	9576	0.05
23	1	E	9525	0.05
23	2	F	9525	0.05
24	1	E	9490	0.05
24	2	G	9490	0.05
25	1	E	9469	0.05
25	2	H	9469	0.05
26	1	F	9553	0.04
26	2	G	9553	0.04
27	1	F	9475	0.04
27	2	H	9475	0.04
28	1	G	9443	0.05
28	2	H	9443	0.05

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	381	-
R_work	0.314	6879	-
obs	-	-	91.3 %

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