PDB-8ap0: ForT Mutant T138V

ID or keywords:

Entry

Database: PDB / ID: 8ap0

Title

ForT Mutant T138V

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: 1.6 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	8ap0.cif.gz	153 KB	Display	PDBx/mmCIF format
PDB format	pdb8ap0.ent.gz		Display	PDB format
PDBx/mmJSON format	8ap0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8ap0_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	8ap0_full_validation.pdf.gz	1.3 MB	Display
Data in XML	8ap0_validation.xml.gz	17.5 KB	Display
Data in CIF	8ap0_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ap/8ap0 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/8ap0	HTTPS FTP

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Related structure data

Related structure data	8aozC 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
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1)

Deposited unit

AAA: Beta-ribofuranosylaminobenzene 5'-phosphate synthase

hetero molecules

37.4 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
74.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.230, 139.042, 109.651
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

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Protein / Sugars , 2 types, 2 molecules AAA

#1: Protein

Beta-ribofuranosylaminobenzene 5'-phosphate synthase

Mass: 36625.352 Da / Num. of mol.: 1 / Mutation: T138V
Source method: isolated from a genetically manipulated source
Details: Genetically mutated T138V / 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

#2: Sugar

ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose

Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₁₃O₁₄P₃

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Non-polymers , 5 types, 315 molecules

#3: Chemical	ChemComp-MYO / 4-azanyl-1~{H}-pyrazole-3,5-dicarboxylic acid Mass: 171.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₅N₃O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.45 Å³/Da / Density % sol: 54.37 % / 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: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 17, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.6→60 Å / Num. obs: 63680 / % possible obs: 100 % / Redundancy: 10.3 % / CC_1/2: 1 / Net I/σ(I): 15
Reflection shell	Resolution: 1.6→1.63 Å / Num. unique obs: 4624 / CC_1/2: 0.8

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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: 1.6→59.865 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.969 / SU B: 6.61 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2034	3300	4.927 %
R_work	0.1567	63680	-
all	0.159	-	-
obs	-	63680	99.997 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 31.414 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.743 Å²	-0 Å²	0 Å²
2-	-	0.822 Å²	-0 Å²
3-	-	-	-1.565 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→59.865 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2513	0	48	310	2871

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	2675
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	2500
X-RAY DIFFRACTION	r_angle_refined_deg	1.47	1.658	3649
X-RAY DIFFRACTION	r_angle_other_deg	1.317	1.578	5737
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.585	5	347
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.693	20.493	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.177	15	392
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.45	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	343
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3067
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	636
X-RAY DIFFRACTION	r_nbd_refined	0.194	0.2	501
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	2241
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	1281
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1164
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	238
X-RAY DIFFRACTION	r_metal_ion_refined	0.367	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.183	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.17	0.2	60
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.114	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	4.678	2.888	1343
X-RAY DIFFRACTION	r_mcbond_other	4.637	2.885	1342
X-RAY DIFFRACTION	r_mcangle_it	5.364	4.331	1681
X-RAY DIFFRACTION	r_mcangle_other	5.365	4.334	1682
X-RAY DIFFRACTION	r_scbond_it	6.799	3.49	1331
X-RAY DIFFRACTION	r_scbond_other	6.8	3.491	1330
X-RAY DIFFRACTION	r_scangle_it	8.1	5.018	1959
X-RAY DIFFRACTION	r_scangle_other	8.1	5.019	1960
X-RAY DIFFRACTION	r_lrange_it	7.188	36.661	2985
X-RAY DIFFRACTION	r_lrange_other	7.041	35.945	2906
X-RAY DIFFRACTION	r_rigid_bond_restr	1.63	3	5174

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6-1.642	0.499	246	0.478	4644	X-RAY DIFFRACTION	100
1.642-1.686	0.405	242	0.444	4553	X-RAY DIFFRACTION	100
1.686-1.735	0.394	208	0.372	4416	X-RAY DIFFRACTION	100
1.735-1.789	0.326	222	0.343	4332	X-RAY DIFFRACTION	100
1.789-1.847	0.302	213	0.268	4137	X-RAY DIFFRACTION	100
1.847-1.912	0.295	231	0.212	4004	X-RAY DIFFRACTION	100
1.912-1.984	0.23	194	0.177	3900	X-RAY DIFFRACTION	100
1.984-2.065	0.228	182	0.145	3779	X-RAY DIFFRACTION	100
2.065-2.157	0.187	175	0.125	3596	X-RAY DIFFRACTION	100
2.157-2.262	0.202	174	0.119	3463	X-RAY DIFFRACTION	100
2.262-2.384	0.192	158	0.108	3290	X-RAY DIFFRACTION	100
2.384-2.529	0.177	194	0.102	3099	X-RAY DIFFRACTION	100
2.529-2.703	0.184	164	0.107	2902	X-RAY DIFFRACTION	100
2.703-2.919	0.174	146	0.107	2749	X-RAY DIFFRACTION	100
2.919-3.197	0.171	122	0.125	2545	X-RAY DIFFRACTION	100
3.197-3.574	0.183	106	0.143	2292	X-RAY DIFFRACTION	100
3.574-4.125	0.143	108	0.124	2046	X-RAY DIFFRACTION	100
4.125-5.048	0.139	104	0.113	1732	X-RAY DIFFRACTION	100
5.048-7.12	0.188	69	0.137	1380	X-RAY DIFFRACTION	100
7.12-10	0.184	40	0.155	807	X-RAY DIFFRACTION	99.8821

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