PDB-3u40: Crystal structure of a purine nucleoside phosphorylase from Entam...

ID or keywords:

Entry

Database: PDB / ID: 3u40

Title

Crystal structure of a purine nucleoside phosphorylase from Entamoeba histolytica bound to adenosine

Components

Purine nucleoside phosphorylase

Keywords

TRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / purine salvage / maltose binding protein / expression rescue / co-crystal

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: 2.05 Å

Authors

Edwards, T.E. / Gardberg, A.S. / 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	Oct 6, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 19, 2011	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 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_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	3u40.cif.gz	532.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3u40.ent.gz	436.7 KB	Display	PDB format
PDBx/mmJSON format	3u40.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/u4/3u40 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/3u40	HTTPS FTP

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Related structure data

Related structure data	3sdsC 3tl6SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3tl6-d 4tti-d 2i4t-1 4d98-1 6kkt-d 6kku-d 6kkr-d 5mx8-1 4ts9-1 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
Related items in Molecule of the Month	#265 - Jan 2022 Golgi Casein Kinase similarity (1)

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

162 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)	86.277, 101.202, 167.264
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

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

NCS ensembles :

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

#1: Protein	Purine nucleoside phosphorylase / PNPase 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: pMBP1 / Production host: Escherichia coli (E. coli) References: UniProt: C4LXG4, purine-nucleoside phosphorylase
#2: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.29 Å³/Da / Density % sol: 46.24 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: EnhiA.01033.a.MB1 PW30572 at 22 mg/mL with 10 mM adenosine against PACT screen condition E5: 0.2 M sodium nitrate, 20% PEG3350, cryoprotectant: 25% ethylene glycol, crystal tracking ID ...Details: EnhiA.01033.a.MB1 PW30572 at 22 mg/mL with 10 mM adenosine against PACT screen condition E5: 0.2 M sodium nitrate, 20% PEG3350, cryoprotectant: 25% ethylene glycol, crystal tracking ID 225630e5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 2.29 Å³/Da / Density % sol: 46.24 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EnhiA.01033.a.MB1 PW30572 at 22 mg/mL with 10 mM adenosine against PACT screen condition E5: 0.2 M sodium nitrate, 20% PEG3350, cryoprotectant: 25% ethylene glycol, crystal tracking ID ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.97949 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Sep 29, 2011

Radiation

Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97949 Å / Relative weight: 1

Reflection

Resolution: 2.05→50 Å / Num. obs: 90147 / % possible obs: 97.9 % / Redundancy: 6.6 % / R_merge(I) obs: 0.104 / Χ²: 1.004 / Net I/σ(I): 16

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.05-2.12	3.6	0.51	2.3	7631	0.905	84.4
2.12-2.21	5.6	0.429	3.8	8788	0.981	96.1
2.21-2.31	6.4	0.343	5.3	8950	0.981	98.7
2.31-2.43	6.7	0.273	7.1	9095	0.982	99.4
2.43-2.58	6.9	0.234	8.7	9117	1.01	99.8
2.58-2.78	7.1	0.172	12.5	9176	1.102	99.8
2.78-3.06	7.2	0.13	15.8	9195	1.064	100
3.06-3.51	7.3	0.084	22.6	9233	0.995	100
3.51-4.42	7.5	0.068	26.1	9312	0.99	100
4.42-50	7.3	0.049	33.1	9650	0.957	99.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3 Å	46.83 Å
Translation	3 Å	46.83 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	2.3.0	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
MxDC		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TL6

3tl6

Resolution: 2.05→50 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.932 / WR_factor R_free: 0.2101 / WR_factor R_work: 0.1729 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8656 / SU B: 7.726 / SU ML: 0.107 / SU R Cruickshank DPI: 0.1986 / SU R_free: 0.1666 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2186	4521	5 %	RANDOM
R_work	0.1798	-	-	-
obs	0.1818	90061	97.69 %	-

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: 102.87 Å² / B_iso mean: 24.9354 Å² / B_iso min: 9.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.36 Å²	0 Å²	0 Å²
2-	-	1.4 Å²	0 Å²
3-	-	-	-0.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10461	0	147	570	11178

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.02	10865
X-RAY DIFFRACTION	r_angle_refined_deg	1.522	1.974	14740
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.118	5	1410
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.407	23.364	437
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.444	15	1625
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.854	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1619
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8306

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms dev position (Å)	Weight position
1	1	A	302	X-RAY DIFFRACTION	0.08	0.05
1	2	B	302	X-RAY DIFFRACTION	0.08	0.05
2	1	A	294	X-RAY DIFFRACTION	0.08	0.05
2	2	C	294	X-RAY DIFFRACTION	0.08	0.05
3	1	A	305	X-RAY DIFFRACTION	0.05	0.05
3	2	D	305	X-RAY DIFFRACTION	0.05	0.05
4	1	A	296	X-RAY DIFFRACTION	0.06	0.05
4	2	E	296	X-RAY DIFFRACTION	0.06	0.05
5	1	A	295	X-RAY DIFFRACTION	0.04	0.05
5	2	F	295	X-RAY DIFFRACTION	0.04	0.05
6	1	B	289	X-RAY DIFFRACTION	0.07	0.05
6	2	C	289	X-RAY DIFFRACTION	0.07	0.05
7	1	B	299	X-RAY DIFFRACTION	0.08	0.05
7	2	D	299	X-RAY DIFFRACTION	0.08	0.05
8	1	B	294	X-RAY DIFFRACTION	0.08	0.05
8	2	E	294	X-RAY DIFFRACTION	0.08	0.05
9	1	B	285	X-RAY DIFFRACTION	0.08	0.05
9	2	F	285	X-RAY DIFFRACTION	0.08	0.05
10	1	C	292	X-RAY DIFFRACTION	0.09	0.05
10	2	D	292	X-RAY DIFFRACTION	0.09	0.05
11	1	C	291	X-RAY DIFFRACTION	0.09	0.05
11	2	E	291	X-RAY DIFFRACTION	0.09	0.05
12	1	C	288	X-RAY DIFFRACTION	0.08	0.05
12	2	F	288	X-RAY DIFFRACTION	0.08	0.05
13	1	D	298	X-RAY DIFFRACTION	0.05	0.05
13	2	E	298	X-RAY DIFFRACTION	0.05	0.05
14	1	D	284	X-RAY DIFFRACTION	0.04	0.05
14	2	F	284	X-RAY DIFFRACTION	0.04	0.05
15	1	E	281	X-RAY DIFFRACTION	0.02	0.05
15	2	F	281	X-RAY DIFFRACTION	0.02	0.05

LS refinement shell

Resolution: 2.05→2.106 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	241	-
R_work	0.232	5045	-
all	-	5286	-
obs	-	-	80.38 %

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	1.3727	-0.4194	-0.0125	0.4017	0.0561	0.7572	-0.0381	-0.0975	0.0362	-0.0066	0.0076	0.0626	0.0074	-0.0365	0.0305	0.0492	-0.0158	0.0104	0.0721	-0.0274	0.1297	-12.339	26.0456	49.8358
2	0.91	0.2011	-0.3081	0.355	0.1262	0.2322	0.0137	0.0004	0.0922	-0.0072	-0.0074	0.0578	0.0012	0.0134	-0.0063	0.0801	-0.0083	-0.0028	0.0898	-0.0109	0.104	2.4862	33.2167	39.506
3	0.5925	0.0483	-0.2425	0.3448	-0.0927	1.0713	0.0118	0.1026	0.0401	-0.0688	-0.1059	0.0197	0.0277	-0.0181	0.0941	0.0965	0.0036	-0.0084	0.105	0.0163	0.0479	13.3593	26.7605	12.2142
4	0.3083	-0.0616	-0.4181	0.281	0.024	0.9565	-0.0182	0.092	-0.0245	-0.0221	-0.0786	0.0053	0.0613	-0.0707	0.0968	0.0945	-0.0111	-0.0054	0.102	-0.0262	0.0601	4.9964	19.5724	20.9616
5	0.4215	-0.0629	0.2929	0.1557	-0.0116	0.603	0.0243	0.0113	-0.0439	-0.0513	-0.0432	-0.0123	-0.0102	0.0173	0.0189	0.0987	-0.0104	0.0122	0.0863	-0.0119	0.0707	31.9178	9.6166	16.1193
6	0.566	1.5306	0.5029	4.7457	0.0056	3.4957	-0.1139	0.0458	0.0358	-0.3948	-0.0709	0.0136	0.043	0.4533	0.1847	0.1481	0.0613	0.0756	0.0999	0.0561	0.0582	41.8406	15.6835	10.6856
7	1.2588	-0.7074	-0.2665	1.037	0.4714	0.4981	-0.0278	-0.1022	-0.0921	0.036	0.0104	-0.1121	-0.0104	0.0823	0.0175	0.0381	0.0045	0.0002	0.0709	0.0198	0.1362	57.8959	3.3704	48.2394
8	0.4292	0.0786	0.2263	0.5021	-0.1277	0.1875	-0.003	-0.0583	-0.0427	-0.0523	0.0154	-0.0544	-0.0058	-0.0449	-0.0124	0.0616	-0.0054	0.0104	0.0937	0.0078	0.1047	41.9719	-0.2972	38.5172
9	0.5703	-0.1619	-0.1088	1.1718	-0.0958	0.4193	-0.0028	-0.1486	-0.1042	0.0187	-0.1169	-0.0292	0.0065	0.0773	0.1197	0.0708	0.0071	-0.0068	0.1132	0.0681	0.0696	36.7577	0.3329	64.8299
10	0.5011	-0.3425	-0.115	0.7449	-0.2572	0.4491	-0.0016	-0.0711	0.0408	0.0358	-0.0152	0.0097	-0.0166	0.0853	0.0168	0.0765	-0.0032	-0.0065	0.1197	0.0055	0.0528	32.6768	13.8697	64.8701
11	0.811	-0.6379	-0.0257	0.6811	0.2243	0.2479	-0.034	-0.0644	-0.0587	0.001	0.009	0.062	-0.0466	-0.0168	0.025	0.0833	0.0019	0.0181	0.1057	-0.0102	0.0751	9.486	23.0522	65.7685
12	11.7013	6.7605	3.151	9.5236	4.6918	2.3191	-1.3974	0.2494	0.1273	0.4088	0.7816	1.2602	0.2346	0.4242	0.6158	0.4585	0.029	0.2749	0.2689	0.0604	0.2862	3.6179	16.2243	75.0192

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 90
2	X-RAY DIFFRACTION	2	A	91 - 238
3	X-RAY DIFFRACTION	3	B	1 - 123
4	X-RAY DIFFRACTION	4	B	124 - 238
5	X-RAY DIFFRACTION	5	C	1 - 207
6	X-RAY DIFFRACTION	6	C	208 - 238
7	X-RAY DIFFRACTION	7	D	-2 - 64
8	X-RAY DIFFRACTION	8	D	65 - 238
9	X-RAY DIFFRACTION	9	E	1 - 124
10	X-RAY DIFFRACTION	10	E	125 - 238
11	X-RAY DIFFRACTION	11	F	1 - 207
12	X-RAY DIFFRACTION	12	F	208 - 238

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