PDB-3tl6: Crystal structure of purine nucleoside phosphorylase from Entamoe...

ID or keywords:

Entry

Database: PDB / ID: 3tl6

Title

Crystal structure of purine nucleoside phosphorylase from Entamoeba histolytica

Components

Purine nucleoside phosphorylase

Keywords

TRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / anaerobic parasitic protozoan / digestive tract cyst / maltose binding protein / MBP / fusion / PNPase / purine metabolism / nucleotide salvage pathway

Function / homology

Function and homology information

uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function

Biological species

Entamoeba histolytica (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.65 Å

Authors

Edwards, T.E. / Clifton, M.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Expression of proteins in Escherichia coli as fusions with maltose-binding protein to rescue non-expressed targets in a high-throughput protein-expression and purification pipeline.
Authors: Hewitt, S.N. / Choi, R. / Kelley, A. / Crowther, G.J. / Napuli, A.J. / Van Voorhis, W.C.

History

Deposition	Aug 29, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 7, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 21, 2011	Group: Database references
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_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	3tl6.cif.gz	504.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3tl6.ent.gz	415.7 KB	Display	PDB format
PDBx/mmJSON format	3tl6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tl6_validation.pdf.gz	480.8 KB	Display	wwPDB validaton report
Full document	3tl6_full_validation.pdf.gz	492 KB	Display
Data in XML	3tl6_validation.xml.gz	46.3 KB	Display
Data in CIF	3tl6_validation.cif.gz	64 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tl/3tl6 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/3tl6	HTTPS FTP

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Related structure data

Related structure data	3sdsC 3u40C 3occS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3u40-d 2i4t-1 6kku-d 2ac7-1 4tti-d 4d98-1 3kvv-d 2qdk-d 6kkt-d 1z38-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: EnhiA.01033.a

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Purine nucleoside phosphorylase

B: Purine nucleoside phosphorylase

C: Purine nucleoside phosphorylase

D: Purine nucleoside phosphorylase

E: Purine nucleoside phosphorylase

F: Purine nucleoside phosphorylase

hetero molecules

160 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	97.970, 86.560, 102.560
Angle α, β, γ (deg.)	90.000, 117.880, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	LYS	LYS	A	A	3 - 238	7 - 242
2	1	GLU	GLU	LYS	LYS	B	B	3 - 238	7 - 242
1	2	MET	MET	LYS	LYS	A	A	1 - 238	5 - 242
2	2	MET	MET	LYS	LYS	C	C	1 - 238	5 - 242
1	3	MET	MET	LYS	LYS	A	A	1 - 238	5 - 242
2	3	MET	MET	LYS	LYS	D	D	1 - 238	5 - 242
1	4	MET	MET	ALA	ALA	A	A	1 - 237	5 - 241
2	4	MET	MET	ALA	ALA	E	E	1 - 237	5 - 241
1	5	MET	MET	ALA	ALA	A	A	1 - 237	5 - 241
2	5	MET	MET	ALA	ALA	F	F	1 - 237	5 - 241
1	6	GLU	GLU	ALA	ALA	B	B	3 - 237	7 - 241
2	6	GLU	GLU	ALA	ALA	C	C	3 - 237	7 - 241
1	7	GLU	GLU	LYS	LYS	B	B	3 - 238	7 - 242
2	7	GLU	GLU	LYS	LYS	D	D	3 - 238	7 - 242
1	8	GLU	GLU	ALA	ALA	B	B	3 - 237	7 - 241
2	8	GLU	GLU	ALA	ALA	E	E	3 - 237	7 - 241
1	9	GLU	GLU	ALA	ALA	B	B	3 - 237	7 - 241
2	9	GLU	GLU	ALA	ALA	F	F	3 - 237	7 - 241
1	10	MET	MET	LYS	LYS	C	C	1 - 238	5 - 242
2	10	MET	MET	LYS	LYS	D	D	1 - 238	5 - 242
1	11	MET	MET	ALA	ALA	C	C	1 - 237	5 - 241
2	11	MET	MET	ALA	ALA	E	E	1 - 237	5 - 241
1	12	MET	MET	ALA	ALA	C	C	1 - 237	5 - 241
2	12	MET	MET	ALA	ALA	F	F	1 - 237	5 - 241
1	13	MET	MET	ALA	ALA	D	D	1 - 237	5 - 241
2	13	MET	MET	ALA	ALA	E	E	1 - 237	5 - 241
1	14	MET	MET	ALA	ALA	D	D	1 - 237	5 - 241
2	14	MET	MET	ALA	ALA	F	F	1 - 237	5 - 241
1	15	MET	MET	ALA	ALA	E	E	1 - 237	5 - 241
2	15	MET	MET	ALA	ALA	F	F	1 - 237	5 - 241

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Purine nucleoside phosphorylase Mass: 26597.541 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI_130960 / Plasmid: pAVA-MBP / Production host: Escherichia coli (E. coli) References: UniProt: C4LXG4, purine-nucleoside phosphorylase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.41 Å³/Da / Density % sol: 48.93 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: EnhiA.01033.a.MB1 PW30575 at 24.4 mg/mL against JCSG+ screen condition H7: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, with 20% ethylene glycol as cryoprotectant, crystal ...Details: EnhiA.01033.a.MB1 PW30575 at 24.4 mg/mL against JCSG+ screen condition H7: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, with 20% ethylene glycol as cryoprotectant, crystal tracking ID 218267h7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 2.41 Å³/Da / Density % sol: 48.93 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: EnhiA.01033.a.MB1 PW30575 at 24.4 mg/mL against JCSG+ screen condition H7: 0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, with 20% ethylene glycol as cryoprotectant, crystal ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.3 / Wavelength: 0.9765 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011

Radiation

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

Radiation wavelength

Wavelength: 0.9765 Å / Relative weight: 1

Reflection

Resolution: 2.65→50 Å / Num. all: 44364 / Num. obs: 43802 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / B_iso Wilson estimate: 54.736 Å² / R_merge(I) obs: 0.067 / Net I/σ(I): 14.52

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.65-2.72		0.506	2.9	13047	3233	99.2
2.72-2.79		0.405	3.44	12869	3178	99.2
2.79-2.87		0.348	4.02	12286	3036	99.2
2.87-2.96		0.282	4.79	12080	2973	98.9
2.96-3.06		0.203	6.55	11634	2890	99.2
3.06-3.17		0.172	7.56	11173	2783	99.2
3.17-3.29		0.14	9.23	10812	2700	98.8
3.29-3.42		0.107	11.69	10192	2576	99
3.42-3.57		0.081	14.59	9641	2478	98.5
3.57-3.75		0.064	17.91	8975	2386	98.6
3.75-3.95		0.055	20.06	8515	2270	98.6
3.95-4.19		0.05	22.11	7799	2109	98
4.19-4.48		0.042	26.63	7248	2029	98.6
4.48-4.84		0.039	28.27	6693	1855	98.5
4.84-5.3		0.04	27.51	6125	1712	98.1
5.3-5.93		0.041	26.05	5536	1564	97.9
5.93-6.84		0.039	27.68	5136	1397	98.9
6.84-8.38		0.034	31.54	4420	1194	98.4
8.38-11.85		0.028	37.12	3412	922	98.7
	11.85	0.027	35.24	1853	517	95.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	45.33 Å
Translation	3 Å	45.33 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.3.0	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
ADSC		data collection
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OCC

3occ

Resolution: 2.65→50 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.915 / WR_factor R_free: 0.2484 / WR_factor R_work: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8048 / SU B: 28.18 / SU ML: 0.277 / SU R Cruickshank DPI: 1.457 / SU R_free: 0.3413 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.457 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2572	2200	5 %	RANDOM
R_work	0.2127	-	-	-
obs	0.2149	43801	98.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 140.06 Å² / B_iso mean: 58.8445 Å² / B_iso min: 22.97 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.26 Å²	0 Å²	2.81 Å²
2-	-	-4.45 Å²	0 Å²
3-	-	-	0.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9889	0	35	86	10010

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.02	10117
X-RAY DIFFRACTION	r_angle_refined_deg	1.225	1.959	13746
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.752	5	1342
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.36	23.401	394
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.046	15	1409
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.738	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1528
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7763

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms dev position (Å)	Weight position
1	1	A	265	X-RAY DIFFRACTION	0.05	0.05
1	2	B	265	X-RAY DIFFRACTION	0.05	0.05
2	1	A	266	X-RAY DIFFRACTION	0.06	0.05
2	2	C	266	X-RAY DIFFRACTION	0.06	0.05
3	1	A	285	X-RAY DIFFRACTION	0.05	0.05
3	2	D	285	X-RAY DIFFRACTION	0.05	0.05
4	1	A	261	X-RAY DIFFRACTION	0.05	0.05
4	2	E	261	X-RAY DIFFRACTION	0.05	0.05
5	1	A	267	X-RAY DIFFRACTION	0.05	0.05
5	2	F	267	X-RAY DIFFRACTION	0.05	0.05
6	1	B	266	X-RAY DIFFRACTION	0.05	0.05
6	2	C	266	X-RAY DIFFRACTION	0.05	0.05
7	1	B	267	X-RAY DIFFRACTION	0.04	0.05
7	2	D	267	X-RAY DIFFRACTION	0.04	0.05
8	1	B	257	X-RAY DIFFRACTION	0.05	0.05
8	2	E	257	X-RAY DIFFRACTION	0.05	0.05
9	1	B	260	X-RAY DIFFRACTION	0.05	0.05
9	2	F	260	X-RAY DIFFRACTION	0.05	0.05
10	1	C	269	X-RAY DIFFRACTION	0.07	0.05
10	2	D	269	X-RAY DIFFRACTION	0.07	0.05
11	1	C	259	X-RAY DIFFRACTION	0.08	0.05
11	2	E	259	X-RAY DIFFRACTION	0.08	0.05
12	1	C	261	X-RAY DIFFRACTION	0.08	0.05
12	2	F	261	X-RAY DIFFRACTION	0.08	0.05
13	1	D	262	X-RAY DIFFRACTION	0.06	0.05
13	2	E	262	X-RAY DIFFRACTION	0.06	0.05
14	1	D	268	X-RAY DIFFRACTION	0.07	0.05
14	2	F	268	X-RAY DIFFRACTION	0.07	0.05
15	1	E	272	X-RAY DIFFRACTION	0.01	0.05
15	2	F	272	X-RAY DIFFRACTION	0.01	0.05

LS refinement shell

Resolution: 2.65→2.719 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.352	178	-
R_work	0.294	2951	-
all	-	3129	-
obs	-	-	99.24 %

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	0.4202	-0.5358	0.0975	1.3334	0.1248	0.4444	-0.1401	0.1039	0.0607	0.2841	-0.0659	-0.0523	0.112	-0.0558	0.206	0.3127	-0.0312	0.1284	0.0689	-0.0281	0.1432	5.5026	-39.9156	-9.7533
2	1.2518	-0.1425	0.642	1.6907	-0.268	0.9137	-0.0508	0.2561	0.1752	-0.0072	-0.0538	0.1212	0.1048	-0.1714	0.1047	0.0394	-0.0624	-0.0148	0.2938	-0.0612	0.1243	-14.1527	-26.847	-28.2598
3	1.0621	0.5628	0.16	1.1168	0.1982	1.1074	0.1346	0.0038	-0.0204	-0.0177	-0.0476	0.1139	-0.0408	-0.3506	-0.087	0.0768	0.071	-0.0467	0.2695	-0.01	0.1008	-7.2269	-3.2256	-41.2689
4	0.552	0.3519	0.4107	2.2879	1.0051	1.1314	0.2176	0.0967	-0.0392	-0.103	-0.0246	-0.2967	-0.1559	-0.0279	-0.193	0.2679	0.0491	0.1041	0.053	0.0158	0.1654	19.3523	9.9062	-35.4964
5	1.8895	0.3876	-0.3878	2.5894	-1.276	0.9325	0.0377	0.1016	0.0989	0.111	-0.16	-0.6055	-0.0274	-0.0053	0.1223	0.0575	-0.0453	-0.0621	0.0738	0.0653	0.3432	36.9492	-2.6536	-18.658
6	0.1777	0.5369	-0.2485	1.8871	-0.7806	1.9554	0.0336	-0.0062	-0.1171	0.381	-0.2009	-0.5337	0.0238	-0.0603	0.1674	0.2731	-0.0512	-0.1808	0.1108	0.0937	0.2261	29.1454	-27.7298	-4.4936

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 238
2	X-RAY DIFFRACTION	2	B	3 - 238
3	X-RAY DIFFRACTION	3	C	1 - 238
4	X-RAY DIFFRACTION	4	D	0 - 238
5	X-RAY DIFFRACTION	5	E	1 - 237
6	X-RAY DIFFRACTION	6	F	1 - 237

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