PDB-5ilq: Crystal structure of truncated unliganded Aspartate Transcarbamoy...

ID or keywords:

Entry

Database: PDB / ID: 5ilq

Title

Crystal structure of truncated unliganded Aspartate Transcarbamoylase from Plasmodium falciparum

Components

Aspartate carbamoyltransferase

Keywords

TRANSFERASE /

Plasmodium falciparum /

Malaria /

Aspartate /

Pyrimidine biosynthesis

Function / homology

Function and homology information

aspartate carbamoyltransferase /

aspartate carbamoyltransferase activity / : / amino acid metabolic process /

amino acid binding / 'de novo' pyrimidine nucleobase biosynthetic process / membrane => GO:0016020 /

cytosol /

cytoplasm
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Lunev, S. / Bosch, S.S. / Batista, F.D.A. / Wrenger, C. / Groves, M.R.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum.
Authors: Lunev, S. / Bosch, S.S. / Batista, F.d.A. / Wrenger, C. / Groves, M.R.

History

Deposition	Mar 4, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 8, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2016	Group: Database references
Revision 1.2	Apr 3, 2019	Group: Advisory / Data collection / Source and taxonomy Category: entity_src_gen / pdbx_database_PDB_obs_spr / pdbx_database_proc Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3	Mar 8, 2023	Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	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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Download

PDBx/mmCIF format	5ilq.cif.gz	381.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ilq.ent.gz	316 KB	Display	PDB format
PDBx/mmJSON format	5ilq.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/il/5ilq ftp://data.pdbj.org/pub/pdb/validation_reports/il/5ilq	HTTPS FTP

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Related structure data

Related structure data	1ml4S S: Starting model for refinement
Similar structure data	6fba-d 4dep-2 3csu-d 6kj9-2 2rgw-3 1a3g-d 4wva-2 2rgw-2 Search similar-shape structures by Omokage search (details) 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	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (9)

Deposited unit

A: Aspartate carbamoyltransferase

B: Aspartate carbamoyltransferase

C: Aspartate carbamoyltransferase

hetero molecules

121 kDa, 3 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)	86.980, 103.800, 87.110
Angle α, β, γ (deg.)	90.000, 117.680, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Aspartate carbamoyltransferase / Mass: 40350.762 Da / Num. of mol.: 3 / Fragment: UNP residues 37-375 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: atcasE, MAL13P1.221 / Plasmid: pASK-IBA3-PfATC-Met3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: Q8IDP8, aspartate carbamoyltransferase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / 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: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 200 mM Sodium Sulphate, 5 mM MgSO4, 15-18 % (w/v) PEG 3350 in 100mM bis-Tris Propane pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: Oxford Cryostream - 700 series
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97957
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2014
Radiation	Monochromator: liquid nitrogen cooled channel-cut silicon monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97957 Å / Relative weight: 1
Reflection	Resolution: 2.42→45.03 Å / Num. obs: 45217 / % possible obs: 95.2 % / Redundancy: 2.51 % / B_iso Wilson estimate: 56.64 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.062 / R_sym value: 0.076 / Net I/σ(I): 10.81
Reflection shell	Resolution: 2.42→2.56 Å / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 1.98 / % possible all: 95.6

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
PDB_EXTRACT	3.1	data extraction
Coot		model building
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ML4

1ml4

Resolution: 2.5→45.03 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.93 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.447 / ESU R Free: 0.229
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2502	2136	4.7 %	RANDOM
R_work	0.2083	-	-	-
obs	0.2082	45217	95.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 170.08 Å² / B_iso mean: 65.6806 Å² / B_iso min: 22.62 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→45.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7798	0	23	86	7907

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.019	7962
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	7658
X-RAY DIFFRACTION	r_angle_refined_deg	1.961	1.964	10752
X-RAY DIFFRACTION	r_angle_other_deg	3.787	3	17672
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.341	5	960
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.178	25.122	369
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.218	15	1471
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.989	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	1240
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	8837
X-RAY DIFFRACTION	r_gen_planes_other	0.016	0.02	1785
X-RAY DIFFRACTION	r_mcbond_it	2.821	3.593	3861
X-RAY DIFFRACTION	r_mcbond_other	2.821	3.592	3860
X-RAY DIFFRACTION	r_mcangle_it	4.464	5.372	4814

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.336	169	-
R_work	0.334	3038	-
all	-	3207	-
obs	-	-	91.42 %

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	4.0808	-0.2223	-0.6355	0.57	0.1505	2.0306	0.0601	0.1394	0.4869	0.0181	0.0246	-0.0599	-0.3504	0.159	-0.0846	0.216	-0.0361	-0.0174	0.0877	0.023	0.2257	46.2991	11.896	14.4866
2	3.1714	1.0465	1.6226	1.98	1.5471	4.3255	0.0558	0.1378	-0.6066	0.0431	-0.0377	0.2658	0.6636	-0.1731	-0.0181	0.2298	-0.0072	0.02	0.1714	-0.005	0.2846	31.8861	0.0836	11.5522
3	3.7862	-1.0363	0.4104	0.8094	-0.0645	0.7764	-0.052	0.2213	-0.1739	-0.0422	0.0734	-0.0095	0.1416	0.1546	-0.0214	0.1992	-0.0124	0.0139	0.2107	0.0044	0.1227	51.8518	1.7275	9.6996
4	2.2878	-0.0072	0.1693	3.5802	-0.0216	3.2557	-0.1785	0.104	-0.4875	0.0254	0.1165	-0.0971	0.4406	0.1867	0.0621	0.2118	0.0354	0.0501	0.2521	-0.0394	0.23	62.5163	-9.0916	8.6877
5	3.4025	-1.1217	0.4737	1.4668	-0.2722	1.0631	-0.0656	-0.2399	-0.4449	0.1924	-0.0108	-0.1705	0.3524	0.2691	0.0765	0.3096	0.06	0.0164	0.2583	0.0251	0.2181	56.1337	-6.7848	23.7569
6	1.0769	0.0861	-0.9361	7.1395	5.8911	5.8078	0.4858	-0.4123	0.5717	0.1145	-0.3578	0.4079	-0.3428	0.022	-0.128	0.5078	-0.0824	0.046	0.5016	-0.0578	0.6013	45.4756	19.808	18.1469
7	1.9853	-2.1455	-0.5774	5.2814	2.9718	2.4272	-0.2403	-0.164	0.277	0.3555	0.0748	0.0951	-0.1911	0.2252	0.1655	0.4466	-0.1008	0.0286	0.2847	0.0017	0.3319	33.6651	7.0448	50.6905
8	2.0637	-0.713	-0.7949	2.2024	-0.5095	4.283	0.0948	0.0356	0.044	0.0768	-0.0944	0.224	-0.1989	0.0579	-0.0003	0.1322	-0.0473	-0.0041	0.0222	-0.0174	0.1476	25.3317	5.8563	41.2612
9	2.9012	-2.3884	-0.0142	3.6093	-0.5995	0.8384	0.018	0.2182	-0.4905	-0.4416	-0.097	0.0555	0.3646	0.0942	0.079	0.3134	-0.0052	0.0362	0.1622	0.0029	0.206	33.7121	-4.472	29.9252
10	2.1065	0.7571	-0.9124	0.3441	-0.623	2.0907	-0.1105	0.059	-0.1071	0.0076	-0.0244	-0.0608	0.2117	0.1277	0.1349	0.286	-0.0333	-0.0119	0.028	0.0341	0.1357	25.279	-4.089	48.9537
11	3.4803	-0.7631	1.0453	3.4507	0.3319	3.093	0.0202	0.0709	-0.2686	0.0522	-0.0214	0.1139	0.3604	0.0532	0.0012	0.2699	-0.0419	0.0416	0.0187	0.0148	0.124	19.5149	-14.2563	56.8716
12	1.6471	0.5263	-0.0708	1.3335	-0.364	2.4016	-0.0689	0.1595	-0.1585	-0.0682	0.1319	0.3685	0.3486	-0.506	-0.063	0.2636	-0.0467	0.0112	0.1244	0.0087	0.2301	8.9358	-7.0059	47.2419
13	0.1331	-0.5742	-0.201	5.7108	3.6042	2.6472	-0.0437	-0.0688	0.2458	-0.7234	0.1559	-0.7011	-0.7539	0.0712	-0.1122	0.6234	-0.0561	0.0396	0.4842	-0.0359	0.6148	32.5638	18.1584	44.9565
14	0.241	0.6744	-0.1211	6.9988	-1.3714	2.4178	-0.1191	-0.0173	0.2558	0.0088	0.1623	0.2546	-0.4641	-0.2244	-0.0432	0.2857	0.0446	-0.0398	0.2788	0.0214	0.4455	4.6693	20.5066	17.0965
15	3.2113	0.298	0.3636	2.2997	-1.0734	2.441	-0.0039	0.2289	-0.0349	-0.1494	0.0297	-0.0706	-0.02	-0.0355	-0.0258	0.1615	-0.0144	0.0194	0.0608	0.0135	0.1161	17.0247	12.6931	14.8099
16	1.1443	1.5221	-0.8558	4.3093	-1.6878	2.7622	-0.0184	0.0362	-0.4702	0.008	0.0424	-0.27	0.7041	0.2324	-0.024	0.3398	-0.0251	-0.0773	0.2236	-0.0348	0.3146	12.0139	-3.6494	25.957
17	0.6637	-0.2038	0.4778	1.3442	-0.4757	3.7405	0.0623	0.1466	0.0331	-0.1786	0.0455	0.3753	0.1976	-0.2002	-0.1078	0.1262	-0.0388	-0.0471	0.24	0.0362	0.2581	5.0465	9.7712	8.0423
18	2.4872	0.7087	-1.3056	3.1591	0.4929	2.7711	0.0258	0.3689	-0.2153	-0.3332	-0.0234	0.307	0.1637	-0.2116	-0.0024	0.2247	-0.0411	-0.1336	0.3688	0.0193	0.3602	-1.0336	4.8878	-5.0595
19	1.1935	-0.3031	-0.3546	1.4165	0.4692	4.2151	0.0379	0.4024	-0.2388	-0.2954	0.0943	0.063	0.297	0.1121	-0.1322	0.192	-0.0546	-0.0444	0.2881	0.0039	0.2486	15.2519	7.1876	-3.9162
20	5.6489	-4.3315	-0.0528	7.9957	1.5755	0.5108	0.0415	0.0104	-0.242	-0.1573	-0.0083	0.0057	-0.0868	-0.0234	-0.0332	0.4112	0.0227	-0.0137	0.2334	-0.0027	0.3007	15.8432	28.8199	17.8998

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	47 - 104
2	X-RAY DIFFRACTION	2	A	105 - 161
3	X-RAY DIFFRACTION	3	A	162 - 214
4	X-RAY DIFFRACTION	4	A	215 - 296
5	X-RAY DIFFRACTION	5	A	312 - 370
6	X-RAY DIFFRACTION	6	A	371 - 383
7	X-RAY DIFFRACTION	7	B	44 - 62
8	X-RAY DIFFRACTION	8	B	63 - 109
9	X-RAY DIFFRACTION	9	B	110 - 162
10	X-RAY DIFFRACTION	10	B	163 - 214
11	X-RAY DIFFRACTION	11	B	215 - 275
12	X-RAY DIFFRACTION	12	B	276 - 371
13	X-RAY DIFFRACTION	13	B	372 - 382
14	X-RAY DIFFRACTION	14	C	44 - 62
15	X-RAY DIFFRACTION	15	C	63 - 128
16	X-RAY DIFFRACTION	16	C	129 - 161
17	X-RAY DIFFRACTION	17	C	162 - 214
18	X-RAY DIFFRACTION	18	C	215 - 295
19	X-RAY DIFFRACTION	19	C	296 - 373
20	X-RAY DIFFRACTION	20	C	374 - 383

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