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

ID or keywords:

Entry

Database: PDB / ID: 9jhv

Title

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 343K

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 / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / cytosol
Similarity search - Function

Biological species

Aeropyrum pernix K1 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 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 complex with 5'-Deoxy-5'-methylthioadenosine 353K
Authors: Iizuka, Y. / Kikuchi, M. / Yamauchi, T. / Tsunoda, M.

History

Deposition	Sep 10, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9jhv.cif.gz	151.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9jhv.ent.gz	97.3 KB	Display	PDB format
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Validation report

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

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Related structure data

Related structure data	9jd2C 1wtaS 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

Deposited unit

A: S-methyl-5'-thioadenosine phosphorylase

hetero molecules

31.3 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 at the molecular weight of the trimer
93.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.854, 78.854, 233.369
Angle α, β, γ (deg.)	90, 90, 120
Int Tables number	155
Space group name H-M	H32

Components on special symmetry positions

ID	Model	Components
1	1	A-406- HOH

#1: Protein	S-methyl-5'-thioadenosine phosphorylase / 5'-methylthioadenosine phosphorylase / MTA phosphorylase / MTAP 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 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-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.27136 Å³/Da / Density % sol: 45.8812599 %
Crystal grow	Temperature: 293.2 K / Method: counter-diffusion Details: he mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir ...Details: he mixture of protein solution and agarose 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#200,0.1 M phosphate citrate pH 5.4, 5 mM MTA

Crystal

Density Matthews: 2.27136 Å³/Da / Density % sol: 45.8812599 %

Crystal grow

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

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Data collection

Diffraction

Mean temperature: 343 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: BL-17A / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2024

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.65→44.36 Å / Num. obs: 34102 / % possible obs: 100 % / Redundancy: 10 % / CC_1/2: 0.997 / R_merge(I) obs: 0.141 / R_pim(I) all: 0.068 / R_rim(I) all: 0.157 / Χ²: 1.02 / Net I/σ(I): 10

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
9.04-44.36	7.9	0.052	30.7	242	0.997	0.026	0.059	0.96	98.6
1.65-1.68	10	2.469	1.1	1679	0.339	1.203	2.752	1.05	100

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Processing

Software

Name	Version	Classification
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: 1.65→44.36 Å / Cor.coef. F_o:F_c: 0.985 / Cor.coef. F_o:F_c free: 0.975 / SU B: 4.047 / SU ML: 0.056 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1674	1788	5.243 %
R_work	0.1182	32313	-
all	0.121	-	-
obs	-	34101	99.953 %

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: 28.908 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.329 Å²	-0.165 Å²	-0 Å²
2-	-	-0.329 Å²	-0 Å²
3-	-	-	1.067 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→44.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2142	0	32	55	2229

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	2251
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2124
X-RAY DIFFRACTION	r_angle_refined_deg	1.668	1.819	3069
X-RAY DIFFRACTION	r_angle_other_deg	0.58	1.758	4874
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.961	5	278
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.961	5	26
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.057	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.072	10	356
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.782	10	101
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	339
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2710
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	535
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	355
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.206	0.2	1831
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	1105
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	1201
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.127	0.2	56
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.3	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	110
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.058	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	6.832	2.428	1103
X-RAY DIFFRACTION	r_mcbond_other	6.822	2.428	1103
X-RAY DIFFRACTION	r_mcangle_it	10.245	4.364	1381
X-RAY DIFFRACTION	r_mcangle_other	10.242	4.364	1382
X-RAY DIFFRACTION	r_scbond_it	11.042	3.12	1148
X-RAY DIFFRACTION	r_scbond_other	11.041	3.12	1148
X-RAY DIFFRACTION	r_scangle_it	16.426	5.426	1687
X-RAY DIFFRACTION	r_scangle_other	16.421	5.425	1688
X-RAY DIFFRACTION	r_lrange_it	19.605	24.644	2357
X-RAY DIFFRACTION	r_lrange_other	19.601	24.65	2358
X-RAY DIFFRACTION	r_rigid_bond_restr	4.03	3	4375

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
1.65-1.693	0.269	134	0.264	2347	0.264	2483	0.956	0.948	99.9194	0.265
1.693-1.739	0.271	117	0.251	2319	0.252	2438	0.947	0.954	99.918	0.251
1.739-1.79	0.263	137	0.22	2224	0.222	2361	0.955	0.967	100	0.216
1.79-1.845	0.237	133	0.195	2157	0.197	2290	0.961	0.975	100	0.187
1.845-1.905	0.192	127	0.156	2088	0.158	2215	0.973	0.984	100	0.145
1.905-1.972	0.194	113	0.124	2055	0.128	2168	0.978	0.99	100	0.112
1.972-2.046	0.17	101	0.108	1970	0.111	2071	0.983	0.993	100	0.096
2.046-2.129	0.165	109	0.106	1902	0.109	2011	0.985	0.994	100	0.095
2.129-2.224	0.16	105	0.095	1795	0.098	1900	0.984	0.995	100	0.086
2.224-2.332	0.134	97	0.089	1756	0.091	1853	0.99	0.996	100	0.08
2.332-2.458	0.14	96	0.089	1680	0.092	1777	0.988	0.996	99.9437	0.079
2.458-2.606	0.157	95	0.095	1569	0.098	1664	0.986	0.995	100	0.086
2.606-2.786	0.169	73	0.11	1489	0.113	1563	0.985	0.993	99.936	0.102
2.786-3.008	0.165	78	0.108	1398	0.111	1476	0.983	0.993	100	0.103
3.008-3.293	0.139	72	0.102	1285	0.104	1357	0.989	0.993	100	0.1
3.293-3.68	0.15	55	0.101	1172	0.103	1228	0.987	0.994	99.9186	0.102
3.68-4.244	0.119	47	0.091	1058	0.092	1105	0.991	0.995	100	0.099
4.244-5.186	0.121	43	0.094	900	0.095	943	0.994	0.995	100	0.106
5.186-7.284	0.203	37	0.131	714	0.134	752	0.984	0.991	99.867	0.145
7.284-44.36	0.243	19	0.15	435	0.153	459	0.978	0.982	98.9107	0.168

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