PDB-4kgv: The R state structure of E. coli ATCase with ATP bound

ID or keywords:

Entry

Database: PDB / ID: 4kgv

Title

The R state structure of E. coli ATCase with ATP 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 /

MOLECULAR REPLACEMENT / Resolution: 2.1 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	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	4kgv.cif.gz	382.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4kgv.ent.gz	314.4 KB	Display	PDB format
PDBx/mmJSON format	4kgv.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/kg/4kgv ftp://data.pdbj.org/pub/pdb/validation_reports/kg/4kgv	HTTPS FTP

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Related structure data

Related structure data	4kgxC 4kgzC 4kh0C 4kh1C 1d09S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	7at1-1 2hse-1 4kgx-1 4f04-1 8at1-1 1f1b-1 1at1-1 3mpu-1 1tth-1 2h3e-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 - 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 (1)

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)	121.070, 121.070, 155.490
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-700- 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, 694 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-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 688 / 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: 3.2 Å³/Da / Density % sol: 61.5 %
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:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 9, 2012 / Details: Osmic VariMax Optics

Radiation

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

Radiation wavelength

Wavelength: 1.542 Å / Relative weight: 1

Reflection

Resolution: 2.1→38.4 Å / Num. all: 77283 / Num. obs: 77283 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.34 % / R_merge(I) obs: 0.054 / Net I/σ(I): 11.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.1-2.18	5.3	0.42	3.1	1	100
2.18-2.26	5.26	0.352	3.7	1	100
2.26-2.37	5.34	0.284	4.3	1	100
2.37-2.49	5.35	0.216	5.4	1	100
2.49-2.65	5.36	0.163	6.9	1	100
2.65-2.85	5.36	0.126	8.5	1	100
2.85-3.14	5.4	0.091	11.5	1	100
3.14-3.59	5.41	0.066	15.1	1	99.9
3.59-4.52	5.37	0.051	21.5	1	99.9
4.52-38.4	5.25	0.033	34.4	1	99.8

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Processing

Software

Name	Version	Classification
d*TREK		data scaling
d*TREK	9.9.8.8D	data reduction
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
CrystalClear		data collection
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1D09

1d09

Resolution: 2.1→38.4 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0 / Phase error: 22.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2075	3880	5.02 %
R_work	0.1675	-	-
obs	0.1695	77271	99.94 %
all	-	77271	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 48.3145 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→38.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7098	0	96	688	7882

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7320
X-RAY DIFFRACTION	f_angle_d	1.067	9944
X-RAY DIFFRACTION	f_dihedral_angle_d	14.69	2740
X-RAY DIFFRACTION	f_chiral_restr	0.072	1150
X-RAY DIFFRACTION	f_plane_restr	0.005	1284

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 (%)
2.1-2.1256	0.2676	134	0.2257	2609	X-RAY DIFFRACTION	100
2.1256-2.1525	0.2943	134	0.2144	2566	X-RAY DIFFRACTION	100
2.1525-2.1808	0.2346	120	0.2123	2638	X-RAY DIFFRACTION	100
2.1808-2.2107	0.2555	121	0.2094	2601	X-RAY DIFFRACTION	100
2.2107-2.2423	0.2389	136	0.2082	2591	X-RAY DIFFRACTION	100
2.2423-2.2757	0.2351	126	0.2098	2564	X-RAY DIFFRACTION	100
2.2757-2.3113	0.2442	146	0.2149	2611	X-RAY DIFFRACTION	100
2.3113-2.3492	0.2577	144	0.1989	2606	X-RAY DIFFRACTION	100
2.3492-2.3897	0.248	140	0.2015	2589	X-RAY DIFFRACTION	100
2.3897-2.4331	0.2288	121	0.1986	2616	X-RAY DIFFRACTION	100
2.4331-2.4799	0.2671	141	0.1974	2594	X-RAY DIFFRACTION	100
2.4799-2.5305	0.2437	139	0.1961	2591	X-RAY DIFFRACTION	100
2.5305-2.5855	0.2226	143	0.1933	2627	X-RAY DIFFRACTION	100
2.5855-2.6457	0.2855	148	0.1893	2565	X-RAY DIFFRACTION	100
2.6457-2.7118	0.2557	135	0.1941	2603	X-RAY DIFFRACTION	100
2.7118-2.7851	0.2297	142	0.1804	2601	X-RAY DIFFRACTION	100
2.7851-2.867	0.2492	131	0.1834	2640	X-RAY DIFFRACTION	100
2.867-2.9596	0.2319	138	0.1822	2614	X-RAY DIFFRACTION	100
2.9596-3.0653	0.2513	146	0.1812	2593	X-RAY DIFFRACTION	100
3.0653-3.188	0.2208	127	0.1829	2665	X-RAY DIFFRACTION	100
3.188-3.333	0.1931	149	0.1799	2586	X-RAY DIFFRACTION	100
3.333-3.5086	0.2127	140	0.1663	2643	X-RAY DIFFRACTION	100
3.5086-3.7282	0.1891	143	0.1533	2629	X-RAY DIFFRACTION	100
3.7282-4.0158	0.1982	136	0.1425	2641	X-RAY DIFFRACTION	100
4.0158-4.4194	0.1695	151	0.1327	2654	X-RAY DIFFRACTION	100
4.4194-5.0577	0.1719	160	0.1289	2649	X-RAY DIFFRACTION	100
5.0577-6.3674	0.189	144	0.173	2713	X-RAY DIFFRACTION	100
6.3674-38.4082	0.1819	145	0.1605	2792	X-RAY DIFFRACTION	99

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	-0.0045	-0.0223	0.0048	0.1628	0.0303	0.032	-0.0128	0.1978	0.1832	-0.122	-0.02	0.203	-0.4189	-0.0133	-0.0001	0.2796	0.0504	-0.0726	0.3588	0.1008	0.3703	35.458	43.9564	3.1561
2	-0.0391	-0.015	0.0259	0.2407	0.1645	0.1624	0.1289	0.624	-0.1	-0.7645	0.1452	0.438	-0.1596	-0.6573	0.0143	0.3749	0.0287	-0.1372	0.4661	0.0121	0.3705	34.0852	32.5295	-2.9492
3	1.3022	0.6016	-0.1513	1.3214	0.389	0.299	0.0657	0.0351	0.0528	-0.1403	0.0447	0.031	-0.0611	-0.0156	0	0.212	0.0325	0.0018	0.233	0.0382	0.2206	49.3198	41.5196	10.1394
4	0.3992	-0.1868	-0.395	1.2011	0.0854	0.8583	-0.0153	-0.0495	-0.1579	-0.0304	0.1231	0.5019	-0.1814	-0.1234	0.0418	0.1704	-0.0195	-0.0308	0.3244	0.1166	0.4237	28.3315	28.5135	13.6206
5	0.637	0.4023	0.152	0.3974	0.4158	0.8162	0.0758	-0.7044	-0.4963	-0.1237	-0.2918	0.8053	-0.1896	-1.3166	-0.3923	0.1108	-0.1406	0.134	0.4598	0.3134	0.8428	20.668	27.4765	18.9394
6	0.3311	0.2468	0.0388	0.6225	-0.4274	0.5392	0.1732	-0.3178	-0.1554	0.6089	0.1042	0.4882	-0.16	0.0924	0.0625	0.3236	-0.0129	0.0418	0.4759	0.1417	0.3674	36.9272	28.677	27.3792
7	0.8582	-0.0144	0.0209	1.7067	0.8508	0.3441	-0.3814	-0.3724	-0.6551	1.2107	0.3704	1.0024	0.5758	-0.1644	-0.0059	0.2218	-0.1318	0.0418	0.4018	0.2267	0.8117	30.2083	13.5698	20.7756
8	0.1525	-0.1784	0.1768	0.0238	-0.1185	0.1537	0.1409	-0.2986	-0.4948	0.0081	-0.0015	0.4194	0.1174	-0.2932	0.0031	0.2944	-0.0275	-0.0492	0.2915	0.1522	0.6368	37.8417	15.7528	16.2824
9	0.6369	-0.2329	-0.0025	0.0526	0.0416	0.082	0.0402	0.3232	-0.109	-0.4306	0.0377	0.1323	0.135	-0.0868	-0	0.2366	0.0074	-0.0635	0.3224	0.0264	0.264	41.5413	31.735	0.0708
10	0.4726	0.0171	-0.196	0.8963	0.3594	0.8476	0.018	0.2503	0.0167	0.0616	-0.2126	0.0784	-0.014	-0.2058	-0.0018	0.4452	0.2057	-0.0248	0.5215	-0.1424	0.4306	19.9099	74.8633	31.3316
11	0.5538	-0.8098	-0.773	1.2538	1.2553	1.422	-0.1038	-0.1525	-0.0287	-0.0697	-0.248	0.1327	-0.0036	-0.5501	-0.1533	0.2162	0.1149	-0.026	0.5387	-0.1085	0.4561	24.9398	59.0537	23.3066
12	0.9205	0.6072	0.1373	0.8152	0.2299	0.5392	0.1001	-0.2635	0.1104	0.0852	0.0158	0.0789	-0.0793	-0.0917	0	0.3535	0.0363	0.0328	0.363	-0.0358	0.2746	59.6596	54.5727	78.5376
13	0.7529	0.6093	0.6956	0.8024	-0.0651	0.3905	-0.0416	0.0331	0.035	-0.0415	0.0338	0.0605	-0.0799	-0.0136	0	0.2692	0.0157	0.0233	0.2753	0.0083	0.1879	53.749	47.2324	67.4281
14	0.8966	0.0312	-0.7197	0.1699	-0.1928	0.6029	0.0598	0.0431	0.2078	-0.0426	0.0662	-0.0001	-0.3808	0.0642	0	0.4174	-0.0351	0.0482	0.2828	0.0153	0.3096	70.2361	66.3518	68.0435
15	0.1371	0.0897	0.1074	0.204	0.2105	0.1894	-0.2878	0.4095	0.5824	-0.903	0.2716	0.3651	-0.638	0.161	-0.0017	0.6242	0.0324	0.0259	0.309	0.1086	0.514	67.6701	73.0475	58.1076
16	0.1877	-0.2803	-0.2651	0.2774	0.1933	0.3875	-0.0557	0.598	0.414	-0.1744	0.2066	-0.0051	-0.0714	0.3945	0.0011	0.4658	-0.1032	0.0805	0.4176	0.0562	0.3769	74.8241	62.6767	58.3436
17	0.333	0.0554	-0.3689	1.2287	-0.4831	0.4993	-0.0481	0.4281	0.0556	-0.3042	0.1982	-0.2271	-0.2438	0.1148	-0.0197	0.4516	-0.0992	0.1939	0.551	-0.0252	0.3754	80.4938	61.931	55.3553
18	0.7709	-0.0717	0.6645	0.8883	0.1185	0.4488	0.0884	-0.1217	0.1082	0.0325	-0.0249	-0.0887	-0.0794	0.04	0.0001	0.3089	-0.0163	0.0595	0.288	-0.0357	0.2682	73.1752	54.5135	72.0204
19	1.4091	-0.1269	0.6728	1.1877	0.9018	1.2621	-0.3363	-0.264	-0.0613	0.6163	0.0394	-0.1947	-0.1112	0.0035	-0.0234	0.7598	0.2225	-0.026	0.4704	-0.0837	0.3877	24.8414	79.4013	48.0063
20	1.3522	-0.3332	0.4213	0.2269	-0.4073	1.3047	-0.5451	0.0528	0.3023	-0.1632	-0.0197	-0.0391	-0.6812	0.0644	-0.4757	0.6688	0.0743	-0.2475	0.3632	0.0672	0.4314	45.3175	68.3439	55.3827

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 134 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 135 through 195 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 196 through 223 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 224 through 242 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 243 through 261 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 262 through 284 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 285 through 310 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 9 through 67 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 68 through 153 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1 through 53 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 54 through 134 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 135 through 187 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 188 through 215 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 216 through 236 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 237 through 261 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 262 through 310 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 9 through 95 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 96 through 153 )

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Protein , 2 types, 4 molecules ACBD

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