PDB-9jd2: Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylas...

ID or keywords:

Entry

Database: PDB / ID: 9jd2

Title

Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K

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: 1.62 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	Aug 30, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 18, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 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	9jd2.cif.gz	149.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9jd2.ent.gz	96.3 KB	Display	PDB format
PDBx/mmJSON format	9jd2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9jd2_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	9jd2_full_validation.pdf.gz	1.1 MB	Display
Data in XML	9jd2_validation.xml.gz	13.6 KB	Display
Data in CIF	9jd2_validation.cif.gz	17.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jd/9jd2 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/9jd2	HTTPS FTP

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Related structure data

Related structure data	9jhvC 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

31.2 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, The protein was eluted near the molecular weight of the trimer when purified by gel filtration chromatography, so this protein appears to be a trimer.
93.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.048, 79.048, 233.48
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: 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-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.: 47 / 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: 2.28 Å³/Da / Density % sol: 46.172 %
Crystal grow	Temperature: 293.2 K / Method: counter-diffusion / pH: 5.4 Details: The 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: The 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: 2.28 Å³/Da / Density % sol: 46.172 %

Crystal grow

Temperature: 293.2 K / Method: counter-diffusion / pH: 5.4
Details: The 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: 353 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 2, 2024

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.62→39.52 Å / Num. obs: 36182 / % possible obs: 100 % / Redundancy: 9.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.141 / R_pim(I) all: 0.069 / R_rim(I) all: 0.157 / Χ²: 0.85 / Net I/σ(I): 9.8

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
8.87-39.52	8	0.03	25.8	259	0.999	0.015	0.033	0.3	97.4
1.62-1.65	10	2.545	1.1	1763	0.344	1.246	2.838	0.93	100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.77)	refinement
Coot		model building
MOLREP		phasing
Aimless		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1WTA

1wta

Resolution: 1.62→38.944 Å / Cor.coef. F_o:F_c: 0.985 / Cor.coef. F_o:F_c free: 0.973 / SU B: 3.878 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1676	1820	5.03 %
R_work	0.1228	34362	-
all	0.125	-	-
obs	-	36182	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: 28.651 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.31 Å²	-0.155 Å²	0 Å²
2-	-	-0.31 Å²	0 Å²
3-	-	-	1.005 Å²

Refinement step

Cycle: LAST / Resolution: 1.62→38.944 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2142	0	25	47	2214

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	2245
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2116
X-RAY DIFFRACTION	r_angle_refined_deg	1.688	1.819	3064
X-RAY DIFFRACTION	r_angle_other_deg	0.591	1.759	4854
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.903	5	278
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.261	5	26
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.018	5	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.925	10	356
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.216	10	101
X-RAY DIFFRACTION	r_chiral_restr	0.087	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	0.217	0.2	348
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.201	0.2	1778
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	1103
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	1162
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	49
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.233	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.218	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.175	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	7.218	2.404	1103
X-RAY DIFFRACTION	r_mcbond_other	7.217	2.404	1103
X-RAY DIFFRACTION	r_mcangle_it	10.841	4.323	1381
X-RAY DIFFRACTION	r_mcangle_other	10.838	4.323	1382
X-RAY DIFFRACTION	r_scbond_it	10.958	3.098	1142
X-RAY DIFFRACTION	r_scbond_other	10.957	3.097	1142
X-RAY DIFFRACTION	r_scangle_it	16.317	5.388	1682
X-RAY DIFFRACTION	r_scangle_other	16.312	5.386	1683
X-RAY DIFFRACTION	r_lrange_it	20.207	24.485	2336
X-RAY DIFFRACTION	r_lrange_other	20.203	24.491	2337
X-RAY DIFFRACTION	r_rigid_bond_restr	4.187	3	4361

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
1.62-1.662	0.322	131	0.289	2486	0.291	2617	0.935	0.944	100	0.283
1.662-1.707	0.305	138	0.271	2448	0.273	2586	0.928	0.954	100	0.262
1.707-1.757	0.317	122	0.256	2397	0.259	2519	0.938	0.96	100	0.243
1.757-1.811	0.259	120	0.209	2284	0.212	2404	0.959	0.974	100	0.193
1.811-1.87	0.213	113	0.17	2265	0.172	2378	0.973	0.982	100	0.149
1.87-1.936	0.178	130	0.13	2157	0.133	2287	0.982	0.989	100	0.109
1.936-2.008	0.143	113	0.118	2087	0.12	2201	0.988	0.992	99.9546	0.1
2.008-2.09	0.164	109	0.114	2027	0.116	2136	0.987	0.993	100	0.099
2.09-2.183	0.173	99	0.106	1936	0.109	2035	0.983	0.994	100	0.094
2.183-2.289	0.143	103	0.099	1848	0.101	1952	0.987	0.996	99.9488	0.09
2.289-2.412	0.141	93	0.095	1775	0.097	1868	0.988	0.996	100	0.089
2.412-2.558	0.184	79	0.098	1707	0.102	1787	0.982	0.995	99.944	0.092
2.558-2.734	0.149	69	0.112	1604	0.114	1675	0.987	0.992	99.8806	0.112
2.734-2.952	0.149	77	0.108	1454	0.11	1531	0.987	0.993	100	0.111
2.952-3.232	0.134	74	0.106	1378	0.107	1452	0.989	0.993	100	0.113
3.232-3.61	0.12	64	0.096	1255	0.097	1319	0.991	0.994	100	0.107
3.61-4.163	0.121	48	0.092	1118	0.093	1166	0.992	0.995	100	0.109
4.163-5.084	0.136	53	0.097	942	0.099	996	0.99	0.995	99.8996	0.123
5.084-7.129	0.204	54	0.127	743	0.132	797	0.983	0.993	100	0.16
7.129-38.944	0.177	31	0.149	451	0.151	488	0.984	0.986	98.7705	0.209

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