PDB-4kgx: The R state structure of E. coli ATCase with CTP bound

ID or keywords:

Entry

Database: PDB / ID: 4kgx

Title

The R state structure of E. coli ATCase with CTP bound

Components

Aspartate carbamoyltransferase
Aspartate carbamoyltransferase regulatory chain

Keywords

TRANSFERASE / pyrimidine nucleotide biosynthesis / feedback inhibition / competing pathway product activation / allostery

Function / homology

Function and homology information

Aspartate carbamoyltransferase regulatory subunit, N-terminal domain / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Aspartate/ornithine carbamoyltransferase / SH3 type barrels. / Roll / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.202 Å

Authors

Cockrell, G.M. / Zheng, Y. / Guo, W. / Peterson, A.W. / Kantrowitz, E.R.

Citation

Journal: Biochemistry / Year: 2013
Title: New Paradigm for Allosteric Regulation of Escherichia coli Aspartate Transcarbamoylase.
Authors: Cockrell, G.M. / Zheng, Y. / Guo, W. / Peterson, A.W. / Truong, J.K. / Kantrowitz, E.R.

History

Deposition	Apr 29, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 27, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2	Sep 20, 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 / 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	4kgx.cif.gz	376 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4kgx_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4kgx_full_validation.pdf.gz	1.7 MB	Display
Data in XML	4kgx_validation.xml.gz	41.3 KB	Display
Data in CIF	4kgx_validation.cif.gz	59.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kg/4kgx ftp://data.pdbj.org/pub/pdb/validation_reports/kg/4kgx	HTTPS FTP

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Related structure data

Related structure data	4kgvC 4kgzC 4kh0C 4kh1C 1d09S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4kgv-1 8at1-1 2hse-1 7at1-1 2h3e-1 2a0f-1 1f1b-1 4f04-1 1at1-1 3mpu-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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 (2)

Deposited unit

A: Aspartate carbamoyltransferase

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

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

1

A: Aspartate carbamoyltransferase

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

A: Aspartate carbamoyltransferase

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

A: Aspartate carbamoyltransferase

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase

D: Aspartate carbamoyltransferase regulatory chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	121.237, 121.237, 154.772
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	A-702- HOH

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Protein , 2 types, 4 molecules ACBD

#1: Protein	Aspartate carbamoyltransferase / Aspartate transcarbamylase Mass: 34337.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: pyrB, EKO11_4066, KO11_22860 / Production host: Escherichia coli (E. coli) / References: UniProt: E8Y328, aspartate carbamoyltransferase
#2: Protein	Aspartate carbamoyltransferase regulatory chain Mass: 17143.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: pyrI, EKO11_4067, KO11_22855 / Production host: Escherichia coli (E. coli) / References: UniProt: E8Y329, aspartate carbamoyltransferase

#1: Protein

Aspartate carbamoyltransferase / Aspartate transcarbamylase

Mass: 34337.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: pyrB, EKO11_4066, KO11_22860 / Production host:

Escherichia coli (E. coli) / References: UniProt: E8Y328, aspartate carbamoyltransferase

#2: Protein

Aspartate carbamoyltransferase regulatory chain

Mass: 17143.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: ATCC 55124 / KO11 / Gene: pyrI, EKO11_4067, KO11_22855 / Production host:

Escherichia coli (E. coli) / References: UniProt: E8Y329, aspartate carbamoyltransferase

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Non-polymers , 4 types, 689 molecules

#3: Chemical	ChemComp-PAL / N-(PHOSPHONACETYL)-L-ASPARTIC ACID Mass: 255.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₀NO₈P
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₆N₃O₁₄P₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 683 / 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: 3.19 Å³/Da / Density % sol: 61.43 %
Crystal grow	Temperature: 293 K / Method: microdialysis / pH: 5.9 Details: 50 mM maleic acid, 1 mM PALA, 3 mM sodium azide, pH 5.9, Microdialysis, temperature 293K

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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: Oct 19, 2011

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

Resolution: 2.2→50 Å / Num. all: 67084 / Num. obs: 67084 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 22.4 % / R_merge(I) obs: 0.075 / Net I/σ(I): 10.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.2-2.28	18.9	0.647	1	100
2.28-2.37	19.2	0.53	1	100
2.37-2.48	19.5	0.383	1	100
2.48-2.61	20	0.271	1	100
2.61-2.77	20.7	0.198	1	100
2.77-2.99	21.5	0.142	1	100
2.99-3.29	22	0.097	1	100
3.29-3.76	22	0.074	1	100
3.76-4.74	28.2	0.064	1	100
4.74-50	31.9	0.043	1	100

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1D09

1d09

Resolution: 2.202→49.715 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.19 / σ(F): 0 / Phase error: 19.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1924	3395	5.06 %
R_work	0.1559	-	-
obs	0.1578	67071	99.96 %
all	-	67071	-

Solvent computation

Shrinkage radii: 1.3 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 39.2568 Å²

Refinement step

Cycle: LAST / Resolution: 2.202→49.715 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7082	0	92	683	7857

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7298
X-RAY DIFFRACTION	f_angle_d	1.065	9912
X-RAY DIFFRACTION	f_dihedral_angle_d	14.299	2736
X-RAY DIFFRACTION	f_chiral_restr	0.072	1147
X-RAY DIFFRACTION	f_plane_restr	0.004	1283

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 (%)
2.202-2.2332	0.2649	129	0.2073	2617	X-RAY DIFFRACTION	100
2.2332-2.2666	0.2164	145	0.1993	2604	X-RAY DIFFRACTION	100
2.2666-2.302	0.2455	148	0.1977	2610	X-RAY DIFFRACTION	100
2.302-2.3397	0.2363	143	0.1921	2666	X-RAY DIFFRACTION	100
2.3397-2.3801	0.2507	138	0.1805	2605	X-RAY DIFFRACTION	100
2.3801-2.4233	0.2132	152	0.1761	2631	X-RAY DIFFRACTION	100
2.4233-2.4699	0.2168	124	0.1688	2620	X-RAY DIFFRACTION	100
2.4699-2.5204	0.2078	136	0.1597	2638	X-RAY DIFFRACTION	100
2.5204-2.5752	0.2111	134	0.1628	2633	X-RAY DIFFRACTION	100
2.5752-2.6351	0.2169	156	0.1643	2630	X-RAY DIFFRACTION	100
2.6351-2.701	0.2281	153	0.1628	2604	X-RAY DIFFRACTION	100
2.701-2.774	0.2157	141	0.1591	2635	X-RAY DIFFRACTION	100
2.774-2.8556	0.2411	124	0.1598	2635	X-RAY DIFFRACTION	100
2.8556-2.9478	0.2179	137	0.1665	2647	X-RAY DIFFRACTION	100
2.9478-3.0531	0.2196	144	0.1662	2652	X-RAY DIFFRACTION	100
3.0531-3.1753	0.1921	169	0.1651	2621	X-RAY DIFFRACTION	100
3.1753-3.3198	0.2422	133	0.1718	2647	X-RAY DIFFRACTION	100
3.3198-3.4948	0.1835	164	0.1546	2650	X-RAY DIFFRACTION	100
3.4948-3.7137	0.1573	128	0.1476	2668	X-RAY DIFFRACTION	100
3.7137-4.0003	0.1605	141	0.1438	2682	X-RAY DIFFRACTION	100
4.0003-4.4027	0.1829	144	0.1306	2679	X-RAY DIFFRACTION	100
4.4027-5.0392	0.1771	132	0.1282	2714	X-RAY DIFFRACTION	100
5.0392-6.3468	0.1666	145	0.1676	2730	X-RAY DIFFRACTION	100
6.3468-49.7278	0.1677	135	0.1503	2858	X-RAY DIFFRACTION	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	0.0047	-0.007	0.0029	0.0058	-0.0046	0.0145	-0.0086	0.0272	0.0099	-0.0249	-0.0328	0.0092	-0.0222	0.0154	-0.0323	0.1078	0.1106	-0.0933	0.1607	0.1582	0.287	35.5951	44.1689	3.1506
2	0.0116	-0.001	-0.0027	0.004	-0.0023	0.0048	-0.0102	0.0278	-0.0076	-0.0113	0.0123	0.0099	-0.0173	-0.0124	0.009	0.077	0.0317	-0.1539	0.1723	-0.0136	0.1744	34.2079	32.7382	-2.9601
3	0.0124	-0.0119	-0.0075	0.0093	0.009	0.0041	-0.0149	0.0893	0.0452	-0.0656	0.0616	-0.0171	-0.0316	-0.0004	0.0193	0.1494	0.0033	0.0081	0.1658	0.035	0.1203	50.667	36.8009	2.4508
4	0.1529	-0.0413	-0.0386	0.1081	0.0559	0.1702	0.0667	-0.0526	0.0909	-0.0355	0.0225	0.0361	-0.0242	0.0083	0.1831	0.0932	0.026	0.0211	0.1158	0.0203	0.1458	49.1184	42.9635	12.2376
5	0.0381	0.0361	0.0042	0.1135	0.0307	0.0426	0.0262	-0.0151	-0.1623	-0.0185	0.0925	0.2659	0.0188	-0.0505	0.1233	-0.0368	-0.0286	-0.018	0.2078	0.1079	0.4107	28.4706	28.5372	11.7876
6	0.0096	0.0078	0.0032	0.0083	0.01	0.023	-0.0154	-0.0185	0.0282	0.0126	-0.0169	0.0704	0.0049	-0.0183	-0.0361	0.0641	0.0533	0.1355	0.3242	0.1419	0.3513	23.7042	35.2104	22.4294
7	0.0234	0.0109	-0.0296	0.0031	-0.0131	0.0353	-0.0132	-0.0128	-0.0506	0.0167	-0.0291	0.035	0.0601	-0.0476	-0.0354	0.0356	-0.0833	0.0726	0.1977	0.2356	0.6093	22.6869	22.0849	18.3871
8	0.0147	0.0141	-0.012	0.0111	-0.0124	0.0101	0.0277	-0.0622	-0.0575	0.0805	-0.0051	0.0343	0.0143	0.0141	0.0465	0.1984	0.0263	0.1311	0.3572	0.2171	0.1386	37.1426	26.482	29.691
9	0.0221	-0.0365	-0.0005	0.0586	-0.001	-0.0006	-0.0228	-0.0267	-0.0927	0.0258	0.0123	0.0615	0.0369	-0.0197	-0.0286	0.0633	-0.0884	0.0383	0.0437	0.2259	0.5651	34.4748	14.2875	15.882
10	0.0266	-0.0185	-0.032	0.0853	0.0332	0.0454	0.0188	0.085	-0.0834	-0.1072	0.0274	0.0357	-0.0391	-0.0239	0.0258	0.0467	0.0105	-0.0902	0.1189	0.0373	0.1722	41.6609	31.9771	0.0499
11	0.0055	-0.005	0.0076	0.0051	-0.0076	0.0134	-0.0173	0.0287	0.022	0.0086	-0.0411	0.0187	-0.0064	-0.027	-0.0214	0.2948	0.1912	-0.0166	0.2989	-0.0763	0.2715	16.8334	76.7933	29.6537
12	0.0231	0.0096	-0.0187	0.0168	-0.0054	0.023	-0.0669	0.0156	-0.0494	0.048	-0.0474	0.045	0.0338	0.0044	-0.0595	0.3283	0.3572	-0.0105	0.4462	-0.2261	0.2424	21.0538	74.2239	31.7775
13	0.0423	0.0098	-0.0455	0.0045	-0.0109	0.0488	-0.0746	0.0443	-0.0706	-0.0525	-0.0394	-0.0049	-0.0406	-0.0754	-0.0473	0.1925	0.2926	-0.095	0.4849	-0.2288	0.3738	18.3692	69.8478	20.985
14	0.007	0.0057	-0.0104	0.0232	-0.011	0.0129	-0.0484	-0.1201	0.0197	0.0712	-0.0422	0.1627	0.0534	-0.0938	-0.0234	0.0756	0.0338	0.0732	0.3188	-0.0743	0.3428	30.3047	51.2303	24.8735
15	0.0189	-0.0061	0.01	0.0225	0.0071	0.0145	0.0744	-0.1704	0.121	0.0892	0.0373	0.0567	-0.0699	-0.041	0.1182	0.2169	0.034	0.0296	0.2675	-0.0144	0.0908	59.6836	54.6116	78.2372
16	0.0319	-0.0028	-0.0425	0.0712	0.0161	0.1045	0.0349	0.0521	0.0853	-0.0792	0.0037	0.0335	-0.148	0.0152	0.1352	0.2077	0.0172	0.0327	0.2025	0.029	0.0942	59.0477	52.3152	67.702
17	0.0498	-0.0081	0.0059	0.0214	-0.0195	0.0367	0.0191	0.2913	0.2217	-0.2539	0.0806	0.0144	-0.1161	-0.0156	0.03	0.4165	-0.0503	0.0975	0.2517	0.0657	0.2335	69.8625	67.8933	59.0367
18	0.0049	0.003	-0.0078	0.0002	-0.003	0.0146	0.0041	0.0396	0.013	-0.0498	-0.028	-0.0384	0.0019	0.0005	-0.004	0.3361	-0.126	0.2255	0.3999	-0.0958	0.2636	84.7687	63.1731	58.8509
19	0.0387	0.0096	0.0189	0.0699	-0.0202	0.0155	-0.0053	-0.0688	0.0205	0.061	-0.0217	-0.0745	-0.0317	-0.0571	-0.0367	0.2496	-0.0263	0.0681	0.2635	-0.0203	0.1617	73.2092	54.5932	71.7426
20	0.0626	-0.0935	-0.065	0.1741	0.1215	0.0862	-0.1539	-0.0894	-0.0257	0.2787	-0.0018	0.0681	0.0804	0.0233	-0.1332	0.6052	0.2822	-0.0524	0.3529	-0.107	0.1893	26.1897	78.7589	47.0727
21	0.0016	0.0027	0.0009	0.0089	0.0058	0.0224	0.0075	-0.0396	0.0038	0.0568	-0.0601	0.0137	-0.0134	-0.0088	0.0001	0.7875	0.3294	-0.1566	0.4892	-0.1738	0.4246	28.8366	81.2206	57.208
22	0.0306	0.0008	-0.0231	0.0377	0.0086	0.0257	-0.0661	-0.0188	0.0365	-0.0223	-0.0218	0.0396	0.0071	0.0339	-0.0557	0.3759	0.0639	-0.1813	0.2529	0.0876	0.1838	45.9581	65.8576	54.7534
23	0.0009	0.0041	-0.0026	0.0157	-0.0063	0.002	-0.0601	0.0379	0.0262	-0.0406	-0.0158	-0.0068	-0.0181	0.0224	-0.045	0.4593	-0.0033	-0.1519	0.2369	0.1672	0.2713	48.3667	68.1957	53.7608

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 16 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 32 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 33 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 134 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 135 through 187 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 188 through 204 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 205 through 227 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 228 through 250 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 251 through 284 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 285 through 310 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 9 through 25 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 26 through 67 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 68 through 104 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 105 through 153 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1 through 53 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 54 through 166 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 167 through 242 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 243 through 261 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 262 through 310 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 11 through 87 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 88 through 104 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 105 through 134 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 135 through 153 )

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