PDB-4fyv: Aspartate Transcarbamoylase Complexed with dCTP

ID or keywords:

Entry

Database: PDB / ID: 4fyv

Title

Aspartate Transcarbamoylase Complexed with dCTP

Components

(Aspartate carbamoyltransferase ...

) x 2

Keywords

TRANSFERASE /

Allosteric Regulation /

Aspartate Carbamoyltransferase /

Escherichia coli

Function / homology

Function and homology information

aspartate carbamoyltransferase complex / pyrimidine nucleotide biosynthetic process /

aspartate carbamoyltransferase /

aspartate carbamoyltransferase activity /

amino acid binding / glutamine metabolic process / protein homotrimerization / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / zinc ion binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.0976 Å

Authors

Cockrell, G.M. / Kantrowitz, E.R.

Citation

Journal: Biochemistry / Year: 2012
Title: Metal Ion Involvement in the Allosteric Mechanism of Escherichia coli Aspartate Transcarbamoylase.
Authors: Cockrell, G.M. / Kantrowitz, E.R.

History

Deposition	Jul 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 10, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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	4fyv.cif.gz	376.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4fyv.ent.gz	309.9 KB	Display	PDB format
PDBx/mmJSON format	4fyv.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/fy/4fyv ftp://data.pdbj.org/pub/pdb/validation_reports/fy/4fyv	HTTPS FTP

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Related structure data

Related structure data	4fywC 4fyxC 4fyyC C: citing same article (ref.)
Similar structure data	4at1-1 1nbe-1 9atc-1 6at1-1 1rai-1 1tu0-1 4fyx-1 1sku-1 5at1-1 2qg9-1 Search similar-shape structures by Omokage search (details) 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 (18)

Deposited unit

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

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

1

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

defined by author&software
312 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	120.680, 120.680, 142.523
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	A-597- HOH
2	1	C-559- HOH
3	1	C-606- HOH

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Aspartate carbamoyltransferase ... , 2 types, 4 molecules ACBD

#1: Protein	Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase Mass: 34337.105 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A786, aspartate carbamoyltransferase
#2: Protein	Aspartate carbamoyltransferase regulatory chain Mass: 17143.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P0A7F3

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Non-polymers , 4 types, 501 molecules

#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₃P₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.91 Å³/Da / Density % sol: 57.73 %
Crystal grow	Temperature: 298 K / Method: microdialysis / pH: 5.7 Details: 40 mM sodium citrate, 1 mM 2-mercaptoethanol, 0.2 mM EDTA, 1.0 mM dCTP, pH 5.7, MICRODIALYSIS, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 1.075 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 18, 2012

Radiation

Monochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Redundancy: 23.1 % / Av σ(I) over netI: 31.8 / Number: 1632963 / R_merge(I) obs: 0.107 / Χ²: 0.9 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 70569 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.52	50	100	1	0.093	0.89	31.2
3.59	4.52	100	1	0.106	1.045	26.5
3.14	3.59	100	1	0.086	0.983	22.1
2.85	3.14	100	1	0.1	0.9	22.2
2.65	2.85	100	1	0.127	0.868	22
2.49	2.65	100	1	0.165	0.873	21.7
2.37	2.49	100	1	0.23	0.862	21.5
2.26	2.37	100	1	0.303	0.852	21.4
2.18	2.26	100	1	0.399	0.857	21.2
2.1	2.18	100	1	0.562	0.837	21.1

Reflection

Resolution: 2.0976→50 Å / Num. all: 70569 / Num. obs: 70569 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 23.1 % / R_merge(I) obs: 0.107 / Χ²: 0.9 / Net I/σ(I): 12.2

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.0976-2.18	21.1	0.562	6979	0.837	1	100
2.18-2.26	21.2	0.399	6973	0.857	1	100
2.26-2.37	21.4	0.303	7012	0.852	1	100
2.37-2.49	21.5	0.23	6975	0.862	1	100
2.49-2.65	21.7	0.165	6992	0.873	1	100
2.65-2.85	22	0.127	7021	0.868	1	100
2.85-3.14	22.2	0.1	7026	0.9	1	100
3.14-3.59	22.1	0.086	7092	0.983	1	100
3.59-4.52	26.5	0.106	7116	1.045	1	100
4.52-50	31.2	0.093	7383	0.89	1	100

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
PHENIX		phasing

Refinement

Resolution: 2.0976→49.062 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8556 / SU ML: 0.19 / σ(F): 0 / Phase error: 21.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2152	3564	5.05 %
R_work	0.1751	67001	-
obs	0.1771	70565	99.84 %

Solvent computation

Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 228.07 Å² / B_iso mean: 56.7152 Å² / B_iso min: 19.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.0976→49.062 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7082	0	63	496	7641

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7270
X-RAY DIFFRACTION	f_angle_d	1.122	9870
X-RAY DIFFRACTION	f_chiral_restr	0.076	1144
X-RAY DIFFRACTION	f_plane_restr	0.005	1274
X-RAY DIFFRACTION	f_dihedral_angle_d	15.069	2710

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.0976-2.1263	0.2451	135	0.2158	2550	2685	96
2.1263-2.1567	0.2907	146	0.2129	2648	2794	100
2.1567-2.1889	0.2756	157	0.2053	2622	2779	100
2.1889-2.2231	0.2499	152	0.1949	2684	2836	100
2.2231-2.2595	0.2354	132	0.1945	2630	2762	100
2.2595-2.2985	0.2592	144	0.1933	2667	2811	100
2.2985-2.3403	0.2447	132	0.1977	2657	2789	100
2.3403-2.3853	0.2394	138	0.1919	2643	2781	100
2.3853-2.434	0.2376	143	0.189	2681	2824	100
2.434-2.4869	0.2552	150	0.1881	2635	2785	100
2.4869-2.5447	0.2473	133	0.1785	2685	2818	100
2.5447-2.6084	0.2087	134	0.1882	2668	2802	100
2.6084-2.6789	0.2499	145	0.1865	2672	2817	100
2.6789-2.7577	0.2394	134	0.1879	2683	2817	100
2.7577-2.8467	0.2572	148	0.195	2653	2801	100
2.8467-2.9485	0.2693	140	0.1974	2702	2842	100
2.9485-3.0665	0.2488	159	0.1885	2654	2813	100
3.0665-3.206	0.2313	141	0.1914	2662	2803	100
3.206-3.375	0.2395	141	0.1867	2708	2849	100
3.375-3.5864	0.2049	153	0.1759	2679	2832	100
3.5864-3.8632	0.2114	130	0.1699	2715	2845	100
3.8632-4.2518	0.195	139	0.1478	2717	2856	100
4.2518-4.8666	0.1716	167	0.1417	2720	2887	100
4.8666-6.1295	0.1911	135	0.1668	2764	2899	100
6.1295-49.0756	0.1671	136	0.1674	2902	3038	100

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	0.2083	0.0909	-0.1535	0.2045	0.1061	0.1552	-0.0615	0.1993	-0.0413	-0.1728	0.1437	0.0921	-0.0986	-0.1349	0.0005	0.3251	0.0252	-0.0409	0.4207	0.0244	0.2742	43.0142	36.2077	2.846
2	0.2204	0.1302	-0.0134	0.0748	-0.0129	0.0049	-0.1162	-0.0132	-0.2181	0.0722	0.0804	-0.1938	-0.36	-0.0987	-0.0039	0.375	0.0617	-0.0518	0.3824	0.081	0.2408	54.5015	43.2931	19.4348
3	0.3216	0.0964	-0.0208	0.0502	0.029	0.1591	0.0145	0.117	0.1049	0.0082	0.0417	0.0872	-0.1158	-0.2945	0.0003	0.2686	0.0089	-0.0347	0.4383	0.0121	0.2473	35.4717	36.0137	12.5245
4	0.0868	-0.0246	-0.0563	0.3129	-0.0328	0.1406	-0.177	-0.2245	-0.0951	0.3516	0.2799	0.2776	0.0382	-0.4388	-0	0.3445	0.0116	-0.0088	0.5481	0.0176	0.3779	25.0448	25.5641	22.2165
5	0.4569	-0.5672	0.092	0.7816	-0.2373	0.239	-0.3702	-0.1355	-0.3146	0.2345	0.2078	0.0694	0.1333	-0.3371	-0.122	0.4623	-0.1715	0.0422	0.3618	-0.0081	0.4638	30.8585	14.408	22.4179
6	0.4337	-0.1754	-0.2485	0.2162	0.1947	0.1462	-0.1659	0.2401	-0.0573	-0.1663	0.0676	-0.0803	0.1473	-0.2228	-0.0003	0.3695	-0.0516	-0.0541	0.3822	-0.0084	0.2653	40.2187	24.2335	7.4632
7	0.0976	0.006	-0.0503	0.0213	-0.0485	0.0989	0.158	0.1708	0.0912	-0.353	-0.213	0.2132	-0.3107	-0.1623	-0.1227	1.0283	0.8543	-0.416	0.7281	-0.5067	0.7996	18.7581	78.3023	28.2748
8	0.0139	0.0096	-0.0294	0.0755	0.0189	0.074	-0.0362	-0.0689	0.006	-0.0761	-0.0442	-0.0114	-0.0693	-0.0602	-0.0539	0.7789	0.9487	-0.2407	0.6063	-0.4628	0.5808	27.4494	69.3552	32.2569
9	0.1176	-0.0352	-0.0699	0.0848	0.1001	0.1229	-0.0039	0.1261	0.1575	-0.0745	0.0036	-0.0072	-0.3042	0.0376	0.0742	1.4333	0.6672	-0.3339	0.635	0.0213	0.6383	31.1332	78.2855	25.6164
10	0.0059	-0.0199	0.0068	0.0351	-0.0143	0.0192	-0.0976	-0.0674	0.0839	-0.1891	-0.0279	-0.0694	-0.0348	-0.1289	-0.0907	0.9814	0.94	-0.279	1.066	-0.5659	1.0358	17.1411	76.7262	35.1916
11	0.3519	-0.1373	-0.054	0.1617	-0.046	0.0209	-0.1216	0.2885	-0.2678	-0.2572	0.0041	0.1249	-0.3116	-0.2343	0.014	1.1321	0.9462	-0.6066	0.9045	-0.4316	1.0034	18.206	72.5104	20.601
12	0.5286	0.4126	-0.2958	0.8138	-0.4736	0.3343	0.1077	-0.0818	-0.0545	-0.245	-0.3538	0.1604	-0.3024	-0.2648	-0.136	0.335	0.1536	-0.0445	0.3782	-0.1167	0.2881	32.7121	53.7452	23.4863
13	0.1923	-0.1584	-0.0199	0.128	-0.0231	0.0003	0.17	-0.3055	0.2916	-0.0441	-0.4254	0.7297	0.0374	-0.3561	-0.1812	0.232	0.0458	-0.0037	0.558	-0.265	0.6466	25.534	49.574	26.5364
14	0.4401	0.1676	0.3457	0.298	-0.1663	0.3705	0.1308	-0.1505	0.0934	0.113	-0.0193	-0.0168	-0.119	-0.0267	-0	0.2858	-0.0176	0.0146	0.2433	-0.0297	0.2698	63.1546	52.0084	67.2396
15	0.2462	0.0187	-0.0519	0.1857	-0.0381	0.0562	-0.0411	0.0015	-0.0131	0.0315	0.042	0.0399	-0.0039	-0.0889	0	0.2623	-0.0094	-0.0134	0.2388	-0.0007	0.3019	52.7328	49.4615	55.534
16	0.4725	-0.1746	-0.2811	0.3797	-0.0022	0.2921	0.0598	0.0948	0.2471	-0.1799	-0.071	0.0277	-0.2105	-0.0238	-0	0.3178	-0.0386	-0.052	0.2488	0.0319	0.3253	75.8735	67.2375	54.6561
17	0.0734	-0.0458	-0.0792	0.1063	-0.1002	0.1111	0.2006	-0.0091	0.0578	-0.3612	-0.169	-0.2828	0.0014	-0.0178	-0.0012	0.3634	0.0108	0.0172	0.2798	-0.0001	0.3095	80.2758	58.9031	44.6016
18	0.238	-0.183	0.1344	0.7804	-0.1768	0.1826	-0.0312	-0.0281	-0.0524	0.0265	-0.1356	-0.2045	0.0033	0.0618	0	0.2235	-0.0264	-0.0014	0.2341	-0.0171	0.2834	80.0372	54.1796	59.098
19	0.0282	-0.1002	0.0274	0.3523	0.0652	0.2823	-0.2695	-0.3026	0.3021	-0.3921	0.0195	0.1684	-0.4529	-0.531	-0.1889	1.2087	0.7728	-0.1422	0.1872	-0.008	0.4208	30.4607	82.8826	40.6546
20	1.3265	0.1955	0.6823	0.0537	0.1014	0.3339	0.101	-0.5593	0.1773	-0.2636	-0.1414	0.1943	-0.4416	-0.5396	-0.1093	1.0125	0.3776	-0.1395	0.4134	-0.1434	0.5836	28.3646	82.3875	40.7523
21	0.0341	-0.0775	0.0372	0.8712	-0.2702	0.3956	-0.3481	-0.3498	0.2352	-0.2255	-0.2732	-0.2008	-0.4619	-0.5366	-0.3979	0.8932	0.2992	-0.1365	0.4767	-0.1582	0.6948	35.4976	85.9711	49.1733
22	0.1731	-0.1588	-0.0514	0.1542	0.0118	0.1736	0.161	0.3504	0.1914	-0.1638	-0.0476	0.032	-0.0782	-0.0448	0.0001	0.3555	0.0367	0.0086	0.279	0.0885	0.4174	51.3286	69.2825	45.4841

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:66)	A	1 - 66
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 67:87)	A	67 - 87
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 88:187)	A	88 - 187
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 188:236)	A	188 - 236
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 237:265)	A	237 - 265
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 266:310)	A	266 - 310
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 10:25)	B	10 - 25
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 26:32)	B	26 - 32
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 33:42)	B	33 - 42
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 43:62)	B	43 - 62
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 63:101)	B	63 - 101
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 102:129)	B	102 - 129
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 130:153)	B	130 - 153
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 1:66)	C	1 - 66
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 67:134)	C	67 - 134
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 135:217)	C	135 - 217
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 218:242)	C	218 - 242
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 243:310)	C	243 - 310
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 10:32)	D	10 - 32
20	X-RAY DIFFRACTION	20	chain 'D' and (resseq 33:67)	D	33 - 67
21	X-RAY DIFFRACTION	21	chain 'D' and (resseq 68:101)	D	68 - 101
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 102:153)	D	102 - 153

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