PDB-8aoz: ForT Mutant L24A

ID or keywords:

Entry

Database: PDB / ID: 8aoz

Title

ForT Mutant L24A

Components

Beta-ribofuranosylaminobenzene 5'-phosphate synthase

Keywords

STRUCTURAL PROTEIN / Formycin Biosynthesis pathway protein C-nucleoside formation enzyme

Function / homology

Function and homology information

kinase activity / ATP binding
Similarity search - Function

Biological species

Streptomyces kaniharaensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Li, W. / Naismith, J.H.

Funding support

United Kingdom, 1items

Citation

Journal: Open Biology / Year: 2023
Title: Experimental and computational snapshots of C-C bond formation in a C-nucleoside synthase.
Authors: Li, W. / Girt, G.C. / Radadiya, A. / Stewart, J.J.P. / Richards, N.G.J. / Naismith, J.H.

History

Deposition	Aug 9, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 7, 2022	Provider: repository / Type: Initial release
Revision 1.1	Sep 21, 2022	Group: Data collection / Category: diffrn / Item: _diffrn.ambient_temp
Revision 1.2	Mar 22, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Feb 7, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8aoz.cif.gz	138 KB	Display	PDBx/mmCIF format
PDB format	pdb8aoz.ent.gz		Display	PDB format
PDBx/mmJSON format	8aoz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ao/8aoz ftp://data.pdbj.org/pub/pdb/validation_reports/ao/8aoz	HTTPS FTP

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Related structure data

Related structure data	8ap0C 6yqqS 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

AAA: Beta-ribofuranosylaminobenzene 5'-phosphate synthase

hetero molecules

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

1

AAA: Beta-ribofuranosylaminobenzene 5'-phosphate synthase

hetero molecules

AAA: Beta-ribofuranosylaminobenzene 5'-phosphate synthase

hetero molecules

defined by author
Evidence: gel filtration
75.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.847, 78.847, 110.981
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

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Protein , 1 types, 1 molecules AAA

#1: Protein	Beta-ribofuranosylaminobenzene 5'-phosphate synthase Mass: 36585.246 Da / Num. of mol.: 1 / Mutation: L24A Source method: isolated from a genetically manipulated source Details: Genetically mutated L24A / Source: (gene. exp.) Streptomyces kaniharaensis (bacteria) / Gene: cof6, F7Q99_03185 / Plasmid: pHis-TEV / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): BL21(DE3) pLysE / References: UniProt: A0A5S9CYM0

#1: Protein

Beta-ribofuranosylaminobenzene 5'-phosphate synthase

Mass: 36585.246 Da / Num. of mol.: 1 / Mutation: L24A
Source method: isolated from a genetically manipulated source
Details: Genetically mutated L24A / Source: (gene. exp.)

Streptomyces kaniharaensis (bacteria) / Gene: cof6, F7Q99_03185 / Plasmid: pHis-TEV / Production host:

Escherichia coli BL21 (bacteria) / Variant (production host): BL21(DE3) pLysE / References: UniProt: A0A5S9CYM0

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Non-polymers , 6 types, 132 molecules

#2: Chemical	ChemComp-DPO / DIPHOSPHATE Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MZU / 4-azanyl-3-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-1~{H}-pyrazole-5-carboxylic acid Mass: 339.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₄N₃O₉P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.36 Å³/Da / Density % sol: 47.86 % / Description: Long needle shape crystal
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Bis-Tris Propane [20mM] pH7.0, Glycerol [20%], PEG 8000 [16%], Monopotassium phosphate [40mM] Temp details: Room Temperature

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: Cooled by liquid Nitrogen / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.3776 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 6, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3776 Å / Relative weight: 1
Reflection	Resolution: 1.9→64.28 Å / Num. obs: 28350 / % possible obs: 100 % / Redundancy: 23.2 % / CC_1/2: 1 / R_rim(I) all: 0.106 / Net I/σ(I): 16
Reflection shell	Resolution: 1.9→1.94 Å / Num. unique obs: 1798 / CC_1/2: 0.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6YQQ

6yqq

Resolution: 1.9→64.277 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.954 / WR_factor R_free: 0.202 / WR_factor R_work: 0.163 / SU B: 11.185 / SU ML: 0.151 / Average fsc free: 0.8382 / Average fsc work: 0.8451 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2322	1369	4.838 %
R_work	0.1949	26925	-
all	0.197	-	-
obs	-	28294	99.996 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.488 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.98 Å²	-0 Å²	-0 Å²
2-	-	-0.98 Å²	-0 Å²
3-	-	-	1.959 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→64.277 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2444	0	84	119	2647

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	2621
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.015	2460
X-RAY DIFFRACTION	r_angle_refined_deg	1.424	1.644	3565
X-RAY DIFFRACTION	r_angle_other_deg	1.302	1.573	5642
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.78	5	335
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.327	20.441	136
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.441	15	372
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.747	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	334
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2976
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	613
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	527
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	2197
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	1245
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1129
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	147
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.097	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.211	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.218	0.2	29
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	81
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.11	2.739	1316
X-RAY DIFFRACTION	r_mcbond_other	2.106	2.738	1315
X-RAY DIFFRACTION	r_mcangle_it	2.998	4.098	1647
X-RAY DIFFRACTION	r_mcangle_other	2.998	4.099	1648
X-RAY DIFFRACTION	r_scbond_it	3.119	3.224	1304
X-RAY DIFFRACTION	r_scbond_other	3.12	3.227	1305
X-RAY DIFFRACTION	r_scangle_it	4.419	4.666	1913
X-RAY DIFFRACTION	r_scangle_other	4.418	4.67	1914
X-RAY DIFFRACTION	r_lrange_it	6.952	34.272	2847
X-RAY DIFFRACTION	r_lrange_other	6.952	34.292	2848

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
1.9-1.949	0.395	95	0.421	1970	0.42	2065	0.451	0.462	100	0.383
1.949-2.003	0.417	113	0.38	1872	0.382	1986	0.581	0.591	99.9496	0.34
2.003-2.061	0.358	95	0.359	1856	0.359	1951	0.743	0.663	100	0.313
2.061-2.124	0.323	84	0.315	1814	0.316	1898	0.707	0.768	100	0.265
2.124-2.194	0.302	88	0.28	1743	0.281	1831	0.852	0.847	100	0.228
2.194-2.271	0.28	67	0.245	1705	0.247	1772	0.898	0.88	100	0.2
2.271-2.356	0.252	82	0.215	1640	0.217	1722	0.908	0.919	100	0.168
2.356-2.452	0.227	69	0.194	1581	0.195	1650	0.926	0.938	100	0.143
2.452-2.561	0.249	84	0.212	1510	0.214	1594	0.929	0.929	100	0.161
2.561-2.686	0.273	71	0.189	1445	0.192	1516	0.912	0.945	100	0.14
2.686-2.831	0.246	60	0.175	1412	0.178	1472	0.931	0.949	100	0.135
2.831-3.002	0.236	83	0.174	1299	0.177	1382	0.934	0.953	100	0.14
3.002-3.209	0.189	62	0.178	1246	0.179	1308	0.947	0.954	100	0.148
3.209-3.465	0.238	69	0.178	1155	0.182	1224	0.929	0.952	100	0.159
3.465-3.795	0.24	59	0.18	1076	0.183	1135	0.936	0.954	100	0.164
3.795-4.241	0.192	50	0.172	980	0.174	1030	0.955	0.958	100	0.156
4.241-4.894	0.195	38	0.149	885	0.151	923	0.965	0.969	100	0.14
4.894-5.985	0.216	51	0.174	740	0.177	791	0.96	0.968	100	0.165
5.985-8.427	0.175	25	0.155	613	0.156	638	0.979	0.982	100	0.152
8.427-64.277	0.174	24	0.164	373	0.165	397	0.977	0.977	100	0.187

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	3.2076	0.106	-0.5337	1.4938	-0.0743	1.2565	-0.0235	0.1148	0.2662	-0.1617	0.1375	0.343	-0.0649	-0.3357	-0.1139	0.2332	0.0253	-0.0614	0.1966	0.0455	0.1037	-17.8875	14.5196	8.94
2	3.0856	0.4301	-0.7074	0.6803	0.6454	1.0695	0.0119	0.5398	0.578	-0.3016	0.0988	0.0895	-0.3347	-0.1441	-0.1107	0.3889	0.0262	-0.0234	0.3209	0.0498	0.1209	-4.5803	13.8224	0.5583
3	0.5218	1.8547	-1.5275	6.7507	-5.5342	4.5901	-0.0827	0.0687	0.0779	-0.3272	0.1013	0.018	0.1395	-0.224	-0.0187	0.5455	0.1321	0.0425	0.5606	0.071	0.504	-3.3687	26.1689	17.7552
4	1.815	0.2264	-0.7826	1.1813	-0.1295	2.0463	0.0505	-0.0679	0.249	-0.0667	0.062	0.0174	-0.2753	0.206	-0.1125	0.1951	0.0055	-0.0024	0.1703	-0.0283	0.0368	4.1305	14.7331	17.5669

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	10 - 124
2	X-RAY DIFFRACTION	2	ALL	AAA	125 - 196
3	X-RAY DIFFRACTION	3	ALL	AAA	197 - 212
4	X-RAY DIFFRACTION	4	ALL	AAA	213 - 341

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