PDB-8r3i: Proof of concept study of a probe molecule in TbPTR1

ID or keywords:

Entry

Database: PDB / ID: 8r3i

Title

Proof of concept study of a probe molecule in TbPTR1

Components

Pteridine reductase

Keywords

OXIDOREDUCTASE / PTERIDINE REDUCTASE / TRYPANOSOMATIDS / SHORT-CHAIN DEHYDROGENASE/REDUCTASE

Function / homology

Function and homology information

pteridine reductase activity / nucleotide binding
Similarity search - Function

Biological species

Trypanosoma brucei (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Dawson, A. / GIlbert, I.H. / Montagna, S.

Funding support

United Kingdom, 1items

Citation

Journal: To Be Published
Title: Proof of concept study of a probe molecule in TbPTR1
Authors: Montagna, S. / Gilbert, I.H. / Dawson, A.

History

Deposition	Nov 9, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 20, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8r3i.cif.gz	222.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8r3i.ent.gz	170.1 KB	Display	PDB format
PDBx/mmJSON format	8r3i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r3/8r3i ftp://data.pdbj.org/pub/pdb/validation_reports/r3/8r3i	HTTPS FTP

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Related structure data

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	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Pteridine reductase

B: Pteridine reductase

C: Pteridine reductase

D: Pteridine reductase

hetero molecules

125 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	74.575, 91.939, 82.732
Angle α, β, γ (deg.)	90.000, 115.355, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 268 / Label seq-ID: 16 - 282

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Pteridine reductase Mass: 30200.432 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PTR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-XSH / ~{N}-[(2~{R})-1-[4-[[2,4-bis(azanyl)quinazolin-5-yl]oxymethyl]piperidin-1-yl]-1-oxidanylidene-pent-4-yn-2-yl]ethanamide Mass: 410.470 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₆N₆O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.12 Å³/Da / Density % sol: 0.76 % / Description: block
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Reservoir: 0.1 M bis-tris-propane pH 8.5, 0.2 M sodium acetate, 20 % PEG 3350, 10 % ethane diol Protein: 6 mg/ml in 20 mM tris pH 8, with 1 mM NADPH and 2 mM compound

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95374 Å / Relative weight: 1
Reflection	Resolution: 1.8→67.4 Å / Num. obs: 93231 / % possible obs: 99.8 % / Redundancy: 6.6 % / B_iso Wilson estimate: 18.68 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.067 / R_pim(I) all: 0.043 / Χ²: 0.92 / Net I/σ(I): 13.5
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.513 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4433 / CC_1/2: 0.883 / R_pim(I) all: 0.388 / Χ²: 0.86 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
xia2		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→67.4 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.963 / SU B: 3.308 / SU ML: 0.094 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1903	4778	5.127 %	random
R_work	0.1647	88412	-	-
all	0.166	-	-	-
obs	-	93190	99.797 %	-

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: 23.187 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.708 Å²	0 Å²	-1.005 Å²
2-	-	5.564 Å²	0 Å²
3-	-	-	-2.004 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→67.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7457	0	316	547	8320

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	7908
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	7590
X-RAY DIFFRACTION	r_angle_refined_deg	1.455	1.642	10777
X-RAY DIFFRACTION	r_angle_other_deg	0.489	1.584	17392
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.262	5	988
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.942	5	60
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.392	5	8
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.692	10	1244
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.955	10	304
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	1269
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	9383
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1749
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	1582
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	7073
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	3973
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	4246
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	500
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.05	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.053	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	32
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.146	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	2.213	2.221	3989
X-RAY DIFFRACTION	r_mcbond_other	2.213	2.221	3989
X-RAY DIFFRACTION	r_mcangle_it	3.304	3.962	4964
X-RAY DIFFRACTION	r_mcangle_other	3.304	3.962	4965
X-RAY DIFFRACTION	r_scbond_it	3.108	2.652	3919
X-RAY DIFFRACTION	r_scbond_other	3.108	2.652	3920
X-RAY DIFFRACTION	r_scangle_it	4.925	4.686	5813
X-RAY DIFFRACTION	r_scangle_other	4.925	4.685	5814
X-RAY DIFFRACTION	r_lrange_it	6.165	23.389	8863
X-RAY DIFFRACTION	r_lrange_other	6.146	22.443	8762
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	7773
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.074	0.05	7768
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.073	0.05	7817
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.067	0.05	7849
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.083	0.05	7780
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.073	0.05	7806

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08335	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08335	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07365	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07365	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07308	0.05009
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07308	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06704	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06704	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.0828	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.0828	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.0734	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.0734	0.05009

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 (%)
1.8-1.847	0.285	356	0.293	6361	X-RAY DIFFRACTION	97.5457
1.847-1.897	0.275	360	0.259	6275	X-RAY DIFFRACTION	100
1.897-1.952	0.246	369	0.224	6200	X-RAY DIFFRACTION	99.9544
1.952-2.012	0.241	327	0.209	6031	X-RAY DIFFRACTION	99.9843
2.012-2.078	0.236	335	0.189	5781	X-RAY DIFFRACTION	99.8694
2.078-2.151	0.206	285	0.176	5633	X-RAY DIFFRACTION	99.9831
2.151-2.232	0.2	306	0.166	5435	X-RAY DIFFRACTION	99.9826
2.232-2.323	0.191	290	0.154	5236	X-RAY DIFFRACTION	100
2.323-2.426	0.201	281	0.15	5029	X-RAY DIFFRACTION	100
2.426-2.545	0.183	228	0.153	4817	X-RAY DIFFRACTION	99.9802
2.545-2.682	0.196	213	0.15	4616	X-RAY DIFFRACTION	99.9793
2.682-2.845	0.184	230	0.157	4336	X-RAY DIFFRACTION	100
2.845-3.041	0.192	185	0.152	4103	X-RAY DIFFRACTION	99.9767
3.041-3.284	0.182	213	0.165	3793	X-RAY DIFFRACTION	100
3.284-3.596	0.163	199	0.158	3501	X-RAY DIFFRACTION	100
3.596-4.019	0.169	183	0.149	3157	X-RAY DIFFRACTION	100
4.019-4.638	0.15	178	0.125	2777	X-RAY DIFFRACTION	100
4.638-5.674	0.131	107	0.139	2405	X-RAY DIFFRACTION	100
5.674-7.996	0.2	80	0.156	1858	X-RAY DIFFRACTION	99.9484
7.996-67.4	0.194	53	0.155	1068	X-RAY DIFFRACTION	99.8219

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