PDB-9lye: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylas...

ID or keywords:

Entry

Database: PDB / ID: 9lye

Title

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 100K

Components

S-methyl-5'-thioadenosine phosphorylase

Keywords

TRANSFERASE / MTAP / complex / phosphorylase

Function / homology

Function and homology information

S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / : / purine ribonucleoside salvage / cytosol
Similarity search - Function

Biological species

Aeropyrum pernix K1 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.37 Å

Authors

Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix 100K
Authors: Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.

History

Deposition	Feb 20, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 4, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9lye.cif.gz	157.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9lye.ent.gz	100 KB	Display	PDB format
PDBx/mmJSON format	9lye.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ly/9lye ftp://data.pdbj.org/pub/pdb/validation_reports/ly/9lye	HTTPS FTP

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Related structure data

Related structure data	1wtaS S: Starting model for refinement
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	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: S-methyl-5'-thioadenosine phosphorylase

hetero molecules

32.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: S-methyl-5'-thioadenosine phosphorylase

hetero molecules

A: S-methyl-5'-thioadenosine phosphorylase

hetero molecules

A: S-methyl-5'-thioadenosine phosphorylase

hetero molecules

defined by author&software
Evidence: gel filtration, Elution was observed the molecular weight of the trimer.
97.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.953, 77.953, 231.05
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	155
Space group name H-M	H32

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Protein , 1 types, 1 molecules A

#1: Protein	S-methyl-5'-thioadenosine phosphorylase Mass: 30777.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first M and second F are missing inthe uploaded structure because the electron density could not be observed. Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Gene: mtnP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YAQ8

#1: Protein

S-methyl-5'-thioadenosine phosphorylase

Mass: 30777.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first M and second F are missing inthe uploaded structure because the electron density could not be observed.
Source: (gene. exp.)

Aeropyrum pernix K1 (archaea) / Gene: mtnP / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9YAQ8

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Non-polymers , 5 types, 126 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₅N₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	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: 2.19770145 Å³/Da / Density % sol: 44.0672035 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 15%(v/v)PEG#200, 0.1 M phosphate citrate pH 5.4

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 0.98 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 1.37→43.89 Å / Num. obs: 57204 / % possible obs: 100 % / Redundancy: 10.1 % / CC_1/2: 0.998 / R_merge(I) obs: 0.109 / R_pim(I) all: 0.053 / R_rim(I) all: 0.122 / Χ²: 1.01 / Net I/σ(I): 12.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
7.5-43.89	8.7	0.062	31.7	404	0.996	0.03	0.069	1.11	99.3
1.37-1.39	9	0.873	2.6	2828	0.677	0.454	0.987	0.98	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.82)	refinement
REFMAC	5.8.0430 (refmacat 0.4.82)	refinement
Coot		model building
MOLREP		phasing
Aimless		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1WTA

1wta

Resolution: 1.37→43.89 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.972 / WR_factor R_free: 0.141 / WR_factor R_work: 0.115 / SU B: 1.562 / SU ML: 0.027 / Average fsc free: 0.9826 / Average fsc work: 0.9889 / Cross valid method: FREE R-VALUE / ESU R: 0.045 / ESU R Free: 0.043
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1461	2787	4.872 %
R_work	0.1192	54416	-
all	0.121	-	-
obs	-	57203	99.976 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 14.744 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.046 Å²	0.023 Å²	-0 Å²
2-	-	0.046 Å²	-0 Å²
3-	-	-	-0.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.37→43.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2142	0	108	112	2362

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	2334
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2256
X-RAY DIFFRACTION	r_angle_refined_deg	1.846	1.814	3152
X-RAY DIFFRACTION	r_angle_other_deg	0.644	1.743	5194
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.778	5	288
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.853	5	26
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.188	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.469	10	362
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.763	10	101
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	344
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2730
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	539
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	406
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	2100
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1145
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	1216
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	96
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.177	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.203	0.2	132
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.181	0.2	28
X-RAY DIFFRACTION	r_mcbond_it	3.574	1.141	1107
X-RAY DIFFRACTION	r_mcbond_other	3.567	1.14	1107
X-RAY DIFFRACTION	r_mcangle_it	5.159	2.058	1386
X-RAY DIFFRACTION	r_mcangle_other	5.158	2.059	1387
X-RAY DIFFRACTION	r_scbond_it	7.556	1.61	1227
X-RAY DIFFRACTION	r_scbond_other	7.555	1.612	1228
X-RAY DIFFRACTION	r_scangle_it	10.112	2.706	1758
X-RAY DIFFRACTION	r_scangle_other	10.109	2.708	1759
X-RAY DIFFRACTION	r_lrange_it	12.273	13.671	2511
X-RAY DIFFRACTION	r_lrange_other	12.152	13.371	2491
X-RAY DIFFRACTION	r_rigid_bond_restr	4.382	3	4590

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.37-1.406	0.257	189	0.207	3973	0.209	4163	0.954	0.967	99.976	0.192
1.406-1.444	0.213	211	0.174	3893	0.176	4104	0.968	0.977	100	0.157
1.444-1.486	0.221	181	0.157	3770	0.16	3952	0.967	0.982	99.9747	0.138
1.486-1.532	0.165	183	0.136	3659	0.137	3842	0.982	0.987	100	0.116
1.532-1.582	0.152	168	0.112	3563	0.114	3731	0.984	0.991	100	0.095
1.582-1.637	0.147	171	0.105	3444	0.107	3616	0.985	0.992	99.9723	0.087
1.637-1.699	0.142	159	0.104	3343	0.106	3502	0.986	0.993	100	0.086
1.699-1.768	0.154	158	0.1	3222	0.102	3380	0.985	0.994	100	0.083
1.768-1.847	0.136	155	0.089	3092	0.091	3249	0.989	0.995	99.9384	0.076
1.847-1.937	0.109	156	0.076	2930	0.077	3087	0.992	0.996	99.9676	0.066
1.937-2.041	0.111	141	0.079	2808	0.08	2949	0.993	0.996	100	0.071
2.041-2.165	0.124	152	0.089	2656	0.091	2808	0.99	0.995	100	0.083
2.165-2.314	0.113	142	0.083	2474	0.085	2616	0.992	0.996	100	0.08
2.314-2.498	0.111	116	0.087	2359	0.088	2475	0.992	0.996	100	0.086
2.498-2.736	0.128	100	0.104	2170	0.105	2270	0.99	0.994	100	0.104
2.736-3.057	0.122	113	0.113	1952	0.113	2065	0.991	0.993	100	0.119
3.057-3.528	0.157	100	0.138	1736	0.139	1839	0.985	0.988	99.8369	0.15
3.528-4.314	0.129	81	0.138	1496	0.138	1577	0.99	0.988	100	0.16
4.314-6.071	0.193	67	0.166	1177	0.167	1244	0.983	0.987	100	0.205
6.071-43.89	0.212	44	0.214	699	0.213	745	0.975	0.976	99.7315	0.259

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