PDB-4glj: Crystal structure of methylthioadenosine phosphorylase in complex...

ID or keywords:

Entry

Database: PDB / ID: 4glj

Title

Crystal structure of methylthioadenosine phosphorylase in complex with rhodamine B

Components

RsfP

Keywords

TRANSFERASE / Methylthioadenosine phosphorylase / methylthioadenosine / rhodamine B / methagenomic library / Antarctic soil

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

uncultured bacterium (environmental samples)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.9 Å

Authors

Bujacz, A. / Bujacz, G. / Cieslinski, H. / Bartasun, P.

Citation

Journal: Plos One / Year: 2013
Title: A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an antarctic soil metagenomic library.
Authors: Bartasun, P. / Cieslinski, H. / Bujacz, A. / Wierzbicka-Wos, A. / Kur, J.

History

Deposition	Aug 14, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4glj.cif.gz	131.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4glj.ent.gz	103.8 KB	Display	PDB format
PDBx/mmJSON format	4glj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4glj_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4glj_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4glj_validation.xml.gz	17.9 KB	Display
Data in CIF	4glj_validation.cif.gz	24.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/4glj ftp://data.pdbj.org/pub/pdb/validation_reports/gl/4glj	HTTPS FTP

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Related structure data

Related structure data	4glfSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4glf-1 3i26-2 4u19-d 6dyz-1 6g0y-d 1hjf-1 3tlf-2 3tlf-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: RsfP

hetero molecules

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

1

A: RsfP

hetero molecules

A: RsfP

hetero molecules

A: RsfP

hetero molecules

defined by author&software
99.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	80.260, 80.260, 81.260
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	A-505- HOH

Details

Trimer

#1: Protein	RsfP Mass: 32165.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: rsfP / Plasmid: pBAD-Myc-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: C6KFA4
#2: Chemical	ChemComp-RHB / N-[9-(2-carboxyphenyl)-6-(diethylamino)-3H-xanthen-3-ylidene]-N-ethylethanaminium Mass: 443.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₈H₃₁N₂O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30%PPG400, 75mM MgCl2, BIS-TRIS, 10mM rhodamine B , VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.94 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2010 / Details: mirrors
Radiation	Monochromator: double crystal Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.94 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. all: 160210 / Num. obs: 22360 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / R_merge(I) obs: 0.082 / R_sym value: 0.082 / Net I/σ(I): 14.6
Reflection shell	Resolution: 1.9→2 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.342 / Mean I/σ(I) obs: 4 / R_sym value: 0.342 / % possible all: 75.3

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
REFMAC	5.6.0117	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4GLF

4glf

Resolution: 1.9→50 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.949 / SU B: 6.126 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20421	936	4.2 %	RANDOM
R_work	0.15478	-	-	-
obs	0.15681	21376	94.99 %	-
all	-	22360	-	-

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: 42.303 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.47 Å²	0.74 Å²	0 Å²
2-	-	1.47 Å²	0 Å²
3-	-	-	-2.21 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2180	0	73	180	2433

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.02	2337
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.042	1.994	3194
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.364	5	298
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.476	24.842	95
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.951	15	382
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.062	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.141	0.2	366
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	1765
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	44	-
R_work	0.195	1184	-
obs	-	-	70.66 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.8851	-2.3936	0.3549	3.897	2.0645	2.9718	-0.2995	-0.2434	0.5277	-0.0139	0.178	-0.352	-0.4203	-0.0648	0.1215	0.3481	0.0731	0.0734	0.1644	-0.0278	0.2677	22.9599	50.8603	64.0101
2	4.4562	-1.012	-0.8689	0.9989	0.6904	0.5947	0.0182	-0.31	0.4871	0.2365	-0.0275	0.0164	-0.0167	-0.0723	0.0093	0.3324	0.0742	0.0065	0.0826	-0.0577	0.0897	27.9844	44.2821	66.7928
3	11.8001	-2.3716	-0.0452	0.7199	1.0349	4.8707	-0.3205	-0.2378	0.1553	0.1503	0.0539	0.052	0.0437	-0.3391	0.2666	0.205	0.1555	0.0816	0.1466	0.045	0.0507	23.0513	36.8446	66.4503
4	1.6578	-0.909	0.5077	1.9981	-0.3764	0.6964	-0.0193	0.1353	0.1907	-0.1884	-0.1082	-0.0676	-0.1785	0.0366	0.1275	0.0925	0.0095	-0.0307	0.0234	0.0172	0.0334	30.9734	40.7065	46.9181
5	2.7782	1.9721	-2.342	3.1949	-0.4249	2.8296	-0.0556	-0.2085	-0.1359	0.124	-0.2014	0.104	0.1596	0.1286	0.257	0.023	0.0144	0.0188	0.053	-0.002	0.03	27.1993	24.472	61.1797
6	2.3283	-1.6294	0.876	15.0352	-3.6756	3.6111	-0.1608	0.1219	0.1102	-0.3629	0.3756	0.5783	-0.3017	-0.5853	-0.2148	0.0854	0.0634	-0.0323	0.1537	0.0258	0.0648	20.5589	45.2433	45.3993
7	4.8129	-1.7784	1.2541	3.557	-2.0268	2.3178	-0.0785	0.1481	0.2554	-0.0755	0.0493	0.0636	-0.3227	-0.1346	0.0293	0.117	0.0304	-0.0249	0.0202	0.0086	0.0242	35.3884	40.1794	47.2805
8	20.9152	-2.2532	6.5025	5.5376	2.5838	9.9734	0.0305	0.5232	-0.5601	-0.6916	-0.1464	0.3237	-0.1165	-0.0826	0.1159	0.1055	0.0039	-0.0276	0.0222	-0.021	0.0324	43.3555	31.2109	42.8061
9	4.1208	1.1632	-3.4745	1.2431	-1.1816	2.9799	-0.0224	0.2568	0.0016	0.0504	0.0264	0.07	-0.0097	-0.2162	-0.0039	0.0474	0.0218	-0.028	0.034	-0.0228	0.0292	28.015	33.8038	55.4708
10	6.9379	5.5152	-3.6732	5.4813	-3.2692	8.7729	-0.534	0.0865	-0.1098	-0.2224	0.2896	-0.3778	-0.1157	0.448	0.2444	0.096	0.0078	-0.046	0.0976	-0.0411	0.1023	32.1139	43.3152	48.9103
11	0.0349	-0.0186	0.0022	0.0191	-0.0013	0.0003	-0.0621	-0.1852	0.0686	-0.0775	0.0965	-0.0761	0.0031	-0.0189	-0.0345	1.1406	-0.1979	0.082	1.2762	-0.0268	1.1448	48.9485	47.4781	45.1038
12	17.0263	5.14	-1.6623	6.7244	-0.0064	4.4659	0.1652	-0.6359	0.7618	0.084	-0.1574	-0.0223	-0.5339	0.2127	-0.0078	0.2239	0.0803	-0.0091	0.1061	-0.0116	0.0865	24.2221	51.9353	51.5242
13	0.0052	0.1007	-0.1608	5.8068	-4.6503	6.022	-0.0054	0.0307	0.0002	0.0297	0.2305	0.6631	0.1563	-0.667	-0.2252	0.0544	0.029	0.0606	0.2546	-0.0274	0.1928	14.9321	24.824	65.4641

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	11 - 36
2	X-RAY DIFFRACTION	2	A	37 - 76
3	X-RAY DIFFRACTION	3	A	77 - 90
4	X-RAY DIFFRACTION	4	A	91 - 120
5	X-RAY DIFFRACTION	5	A	121 - 140
6	X-RAY DIFFRACTION	6	A	141 - 160
7	X-RAY DIFFRACTION	7	A	161 - 179
8	X-RAY DIFFRACTION	8	A	180 - 193
9	X-RAY DIFFRACTION	9	A	194 - 212
10	X-RAY DIFFRACTION	10	A	213 - 223
11	X-RAY DIFFRACTION	11	A	224 - 239
12	X-RAY DIFFRACTION	12	A	240 - 265
13	X-RAY DIFFRACTION	13	A	266 - 297

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