PDB-9vs8: Intermediate state structure of 5'-Deoxy-5'-methylthioadenosine p...

ID or keywords:

Entry

Database: PDB / ID: 9vs8

Title

Intermediate state structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix at high temperature (363K) after 10 minutes reaction with substrate

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: 2.08 Å

Authors

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

Funding support

1items

Citation

Journal: To Be Published
Title: Intermediate state structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix at high temperature (363K) after 10 minutes reaction with substrate
Authors: Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.

History

Deposition	Jul 8, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 22, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9vs8.cif.gz	72.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9vs8.ent.gz	50.3 KB	Display	PDB format
PDBx/mmJSON format	9vs8.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vs/9vs8 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/9vs8	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

Deposited unit

A: S-methyl-5'-thioadenosine phosphorylase

hetero molecules

30.9 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.
92.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.042, 79.042, 233.625
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	155
Space group name H-M	H32

#1: Protein	S-methyl-5'-thioadenosine phosphorylase / 5'-methylthioadenosine phosphorylase / MTA phosphorylase / MTAP Mass: 30498.967 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first M and second F are missing in the uploaded structure because the electron density could not be observed. Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Gene: mtnP, APE_1885 / Production host: Escherichia coli (E. coli) References: UniProt: Q9YAQ8, S-methyl-5'-thioadenosine phosphorylase
#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-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H₂O
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: 2.28471565 Å³/Da / Density % sol: 46.1974258 %
Crystal grow	Temperature: 293.2 K / Method: counter-diffusion / pH: 5.4 Details: The mixture of protein solution and agarose, methylcellulose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition ...Details: The mixture of protein solution and agarose, methylcellulose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows. 15%(v/v)PEG#200, 0.1M phosphate citrate pH5.4, 5mM MTA

Crystal

Density Matthews: 2.28471565 Å³/Da / Density % sol: 46.1974258 %

Crystal grow

Temperature: 293.2 K / Method: counter-diffusion / pH: 5.4
Details: The mixture of protein solution and agarose, methylcellulose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition ...

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Data collection

Diffraction

Mean temperature: 363 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: Jul 2, 2025

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.08→44.43 Å / Num. obs: 17322 / % possible obs: 100 % / Redundancy: 10.2 % / CC_1/2: 0.997 / R_merge(I) obs: 0.194 / R_pim(I) all: 0.092 / R_rim(I) all: 0.215 / Χ²: 1.01 / Net I/σ(I): 13.2

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
9.07-44.43	7.7	0.034	44.2	243	0.999	0.017	0.038	0.91	98.3
2.08-2.14	10.7	1.123	2.6	1335	0.674	0.526	1.242	1.03	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
Coot		model building
MOLREP		phasing
Aimless		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1WTA

1wta

Resolution: 2.08→44.43 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.96 / WR_factor R_free: 0.148 / WR_factor R_work: 0.12 / SU B: 4.127 / SU ML: 0.104 / Average fsc free: 0.9702 / Average fsc work: 0.9816 / Cross valid method: FREE R-VALUE / ESU R: 0.164 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1741	894	5.161 %
R_work	0.1439	16428	-
all	0.145	-	-
obs	-	17322	99.954 %

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: 32.015 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.285 Å²	0.143 Å²	-0 Å²
2-	-	0.285 Å²	-0 Å²
3-	-	-	-0.926 Å²

Refinement step

Cycle: LAST / Resolution: 2.08→44.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2142	0	25	30	2197

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2239
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2114
X-RAY DIFFRACTION	r_angle_refined_deg	1.746	1.82	3056
X-RAY DIFFRACTION	r_angle_other_deg	0.564	1.759	4850
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.416	5	278
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.18	5	26
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.055	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.854	10	356
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.683	10	101
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	339
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2696
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	533
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	349
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	1832
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1095
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	1194
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.129	0.2	49
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.092	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	88
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.118	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	2.824	2.703	1097
X-RAY DIFFRACTION	r_mcbond_other	2.821	2.703	1097
X-RAY DIFFRACTION	r_mcangle_it	4.386	4.845	1371
X-RAY DIFFRACTION	r_mcangle_other	4.384	4.846	1372
X-RAY DIFFRACTION	r_scbond_it	4.967	3.481	1142
X-RAY DIFFRACTION	r_scbond_other	4.966	3.481	1142
X-RAY DIFFRACTION	r_scangle_it	8.084	6.039	1682
X-RAY DIFFRACTION	r_scangle_other	8.081	6.037	1683
X-RAY DIFFRACTION	r_lrange_it	10.455	27.765	2331
X-RAY DIFFRACTION	r_lrange_other	10.454	27.774	2331

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
2.08-2.134	0.236	63	0.234	1201	0.234	1264	0.955	0.959	100	0.221
2.134-2.192	0.274	78	0.22	1143	0.224	1221	0.946	0.964	100	0.202
2.192-2.256	0.253	72	0.206	1130	0.209	1203	0.952	0.969	99.9169	0.185
2.256-2.325	0.258	66	0.184	1090	0.188	1156	0.959	0.977	100	0.158
2.325-2.401	0.271	39	0.175	1083	0.178	1122	0.947	0.979	100	0.151
2.401-2.485	0.232	52	0.166	1034	0.169	1086	0.962	0.982	100	0.138
2.485-2.578	0.206	53	0.156	999	0.158	1052	0.973	0.983	100	0.131
2.578-2.683	0.22	58	0.157	956	0.16	1014	0.971	0.984	100	0.131
2.683-2.802	0.184	52	0.153	930	0.155	982	0.983	0.986	100	0.127
2.802-2.938	0.188	48	0.138	892	0.14	940	0.977	0.988	100	0.114
2.938-3.097	0.137	41	0.125	839	0.126	880	0.987	0.99	100	0.105
3.097-3.283	0.155	41	0.132	814	0.133	855	0.982	0.988	100	0.113
3.283-3.509	0.158	37	0.13	760	0.132	797	0.977	0.989	100	0.112
3.509-3.788	0.119	33	0.115	722	0.115	756	0.99	0.991	99.8677	0.103
3.788-4.146	0.14	45	0.109	645	0.111	690	0.987	0.992	100	0.099
4.146-4.631	0.098	31	0.093	600	0.094	631	0.994	0.995	100	0.089
4.631-5.338	0.102	28	0.102	532	0.102	560	0.995	0.995	100	0.097
5.338-6.514	0.132	23	0.141	463	0.14	486	0.991	0.989	100	0.134
6.514-9.115	0.203	22	0.139	365	0.142	387	0.974	0.988	100	0.139
9.115-44.43	0.201	12	0.163	230	0.165	245	0.982	0.985	98.7755	0.161

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