PDB-4f04: A Second Allosteric site in E. coli Aspartate Transcarbamoylase: ...

ID or keywords:

Entry

Database: PDB / ID: 4f04

Title

A Second Allosteric site in E. coli Aspartate Transcarbamoylase: R-state ATCase with UTP bound

Components

(Aspartate carbamoyltransferase ...

) x 2

Keywords

TRANSFERASE /

Allosteric Regulation /

ATCase

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 /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

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

Citation

Journal: Biochemistry / Year: 2012
Title: A second allosteric site in Escherichia coli aspartate transcarbamoylase.
Authors: Peterson, A.W. / Cockrell, G.M. / Kantrowitz, E.R.

History

Deposition	May 3, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.3	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	4f04.cif.gz	373.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4f04.ent.gz	310 KB	Display	PDB format
PDBx/mmJSON format	4f04.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/f0/4f04 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/4f04	HTTPS FTP

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Related structure data

Similar structure data	1at1-1 3mpu-1 2at1-1 1tth-1 7at1-1 4kgv-1 1f1b-1 1acm-1 4kh1-1 4kgz-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 (19)

Deposited unit

A: Aspartate carbamoyltransferase catalytic chain

B: Aspartate carbamoyltransferase regulatory chain

C: Aspartate carbamoyltransferase catalytic chain

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

Unit cell

Length a, b, c (Å)	121.277, 121.277, 155.109
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-586- 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 genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4245, JW4204, pyrB / Plasmid: pEK152 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786, 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: K12 / Gene: b4244, JW4203, pyrI / Plasmid: pEK152 / Production host: Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3, aspartate carbamoyltransferase

#1: Protein

Aspartate carbamoyltransferase catalytic chain / Aspartate transcarbamylase / ATCase

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

Escherichia coli (E. coli) / Strain: K12 / Gene: b4245, JW4204, pyrB / Plasmid: pEK152 / Production host:

Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A786,

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: K12 / Gene: b4244, JW4203, pyrI / Plasmid: pEK152 / Production host:

Escherichia coli (E. coli) / Strain (production host): EK1104 / References: UniProt: P0A7F3,

aspartate carbamoyltransferase

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Non-polymers , 4 types, 297 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-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₅N₂O₁₅P₃ / Comment: UTP*YM
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 291 / 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: 61.54 %
Crystal grow	Temperature: 298 K / Method: microdialysis / pH: 5.95 Details: 50 mM maleic acid, 3 mM sodium azide, 1 mM PALA, adjusted to pH=5.95 with N-ethylmorpholine, 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 315r / Detector: CCD / Date: Jan 18, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.075 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 59217 / Redundancy: 23.2 % / R_merge(I) obs: 0.101 / Net I/σ(I): 33.457

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.3-2.38	20.4	0.698	1	100
2.38-2.48	20.5	0.514	1	99.8
2.48-2.59	20.6	0.343	1	99.9
2.59-2.73	20.8	0.252	1	99.9
2.73-2.9	21.2	0.177	1	100
2.9-3.12	21.6	0.12	1	100
3.12-3.44	22	0.082	1	100
3.44-3.93	22.1	0.063	1	100
3.93-4.95	31.3	0.13	1	100
4.95-50	30.8	0.074	1	100

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.7.3_928	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 / Resolution: 2.3→49.741 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 0 / Phase error: 22.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2067	2990	5.05 %
R_work	0.1729	-	-
obs	0.1747	59188	99.92 %
all	-	59217	-

Solvent computation

Shrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.466 Å² / k_sol: 0.281 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.4969 Å²	-0 Å²	-0 Å²
2-	-	3.4969 Å²	0 Å²
3-	-	-	-6.9939 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→49.741 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7065	0	92	291	7448

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7281
X-RAY DIFFRACTION	f_angle_d	1.082	9888
X-RAY DIFFRACTION	f_dihedral_angle_d	14.445	2717
X-RAY DIFFRACTION	f_chiral_restr	0.073	1146
X-RAY DIFFRACTION	f_plane_restr	0.005	1277

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 (%)
2.3-2.3363	0.2943	131	0.2549	2650	X-RAY DIFFRACTION	100
2.3363-2.3766	0.3073	136	0.2399	2658	X-RAY DIFFRACTION	100
2.3766-2.4198	0.2775	124	0.2349	2626	X-RAY DIFFRACTION	100
2.4198-2.4663	0.2903	124	0.2131	2659	X-RAY DIFFRACTION	100
2.4663-2.5166	0.2439	146	0.1997	2625	X-RAY DIFFRACTION	100
2.5166-2.5714	0.2318	143	0.2025	2650	X-RAY DIFFRACTION	100
2.5714-2.6312	0.2621	166	0.2015	2634	X-RAY DIFFRACTION	100
2.6312-2.697	0.2267	143	0.2031	2679	X-RAY DIFFRACTION	100
2.697-2.7699	0.2296	145	0.1905	2635	X-RAY DIFFRACTION	100
2.7699-2.8514	0.2451	150	0.1927	2640	X-RAY DIFFRACTION	100
2.8514-2.9434	0.2445	133	0.1973	2670	X-RAY DIFFRACTION	100
2.9434-3.0486	0.2442	159	0.2012	2637	X-RAY DIFFRACTION	100
3.0486-3.1706	0.244	154	0.2072	2656	X-RAY DIFFRACTION	100
3.1706-3.3149	0.2407	139	0.2021	2672	X-RAY DIFFRACTION	100
3.3149-3.4896	0.2218	151	0.1923	2660	X-RAY DIFFRACTION	100
3.4896-3.7082	0.1867	144	0.172	2688	X-RAY DIFFRACTION	100
3.7082-3.9944	0.1937	127	0.1633	2697	X-RAY DIFFRACTION	100
3.9944-4.3962	0.1863	132	0.1389	2721	X-RAY DIFFRACTION	100
4.3962-5.0318	0.1415	153	0.1316	2718	X-RAY DIFFRACTION	100
5.0318-6.3375	0.1968	138	0.1699	2746	X-RAY DIFFRACTION	100
6.3375-49.7526	0.188	152	0.1537	2877	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	0.7704	0.2459	-0.5027	0.9079	0.4019	0.5935	0.0019	0.3778	0.1151	-0.4587	0.1202	0.1269	-0.1484	-0.0511	0.0036	0.4169	0.0156	-0.1121	0.4092	0.0947	0.3352	44.1568	36.6032	2.1611
2	1.2507	-0.4088	-0.2589	0.9826	-0.0004	0.9057	0.1013	-0.0125	0.139	-0.1658	0.0485	0.2867	-0.1084	-0.1446	0.0359	0.2372	0.0463	-0.0525	0.3109	0.0973	0.3354	41.6799	39.1164	13.0046
3	0.0811	-0.1606	-0.0399	0.2205	0.0635	0.2345	0.0272	0.0074	0.0634	-0.0543	0.1269	0.6363	0.1679	-0.3079	0.1959	0.2811	-0.0328	-0.1109	0.44	0.2154	0.7199	25.8097	30.5369	13.5809
4	0.4334	0.0265	-0.3044	0.6325	0.221	0.7423	0.0461	-0.4907	-0.7242	-0.1766	0.2052	0.9716	-0.0594	-0.4278	0.1002	0.2213	-0.0254	-0.0018	0.6043	0.2643	1.0964	23.1651	27.2776	19.969
5	0.3875	0.0178	-0.2662	0.2778	-0.1858	0.5819	0.0608	-0.7209	-0.1132	0.4947	0.0784	0.3453	-0.2161	0.1822	0.0438	0.4154	-0.0425	0.0442	0.6094	0.2287	0.5123	37.2918	26.2637	29.5601
6	0.7497	-0.2856	-0.21	0.2349	0.3426	0.3913	-0.1649	-0.4838	-0.9283	0.1874	0.3742	0.6777	0.3705	0.1264	0.1691	0.3401	-0.1463	-0.1161	0.2781	0.2375	1.0018	34.6589	14.0329	15.6778
7	0.4747	-0.035	-0.2484	0.7955	0.1352	0.3346	0.1254	0.37	-0.3911	-0.8663	0.0038	0.153	0.2083	-0.0761	0.1134	0.3574	0.0003	-0.1922	0.4537	0.011	0.3688	41.6639	31.7704	-0.1317
8	0.1652	-0.092	0.0713	0.137	0.0645	0.1269	-0.1739	-0.0972	0.0063	0.0635	-0.2017	0.4259	-0.3573	-0.3797	-0.1374	-0.1137	0.9407	0.1841	0.465	-0.1993	0.6847	18.6543	80.9968	25.7517
9	0.1387	-0.0454	0.106	0.1408	0.1039	0.2506	-0.234	0.3602	-0.2496	0.677	-0.0018	-0.1049	0.0769	0.1194	-0.003	0.7281	0.2141	0.107	0.5416	-0.1009	0.6927	24.5716	72.0389	32.8567
10	0.2258	-0.0118	0.1399	0.1056	-0.1871	0.3595	-0.3077	0.0554	-0.0269	0.5094	-0.2599	0.569	0.0216	-0.3506	-0.0861	0.9651	0.0605	0.3564	0.8508	-0.4434	1.1534	9.9449	71.122	37.1208
11	0.2172	-0.0093	0.134	0.1097	-0.0517	0.1958	0.0711	0.5306	-0.0913	-0.5124	-0.6259	0.6291	-0.3057	-0.6768	-0.0248	0.5695	0.2418	0.0482	0.6856	-0.2638	0.6769	20.0017	71.9763	23.6929
12	1.401	0.1562	-0.815	0.0352	-0.2348	0.9019	-0.5468	-0.0384	0.4041	-0.4677	-0.3326	0.5329	-0.1667	-0.6894	-0.5681	0.5211	0.3786	-0.3221	0.8633	-0.3357	1.2558	18.035	70.4747	19.7621
13	0.2147	-0.1839	-0.1641	0.6068	-0.099	0.115	-0.0678	-0.6935	0.2055	0.3173	-0.051	0.2112	0.1261	-0.1612	-0	0.3085	0.0688	0.0719	0.6319	0.0136	0.6117	30.2563	50.9159	24.8956
14	0.5113	0.3446	-0.0899	0.3492	0.0702	0.1973	0.1032	-0.3296	0.5805	0.4872	-0.0052	0.415	-0.4624	-0.3194	0.0235	0.5681	-0.0071	0.0656	0.5734	-0.1124	0.3604	59.7793	61.0279	79.2349
15	0.1886	0.0037	0.023	0.1894	0.0195	-0.0011	0.0793	-0.3138	-0.1034	0.2333	0.1003	-0.0285	0.2236	-0.0202	-0.0001	0.4756	-0.0372	-0.0119	0.5967	0.0502	0.315	59.9118	45.0782	76.9285
16	0.686	0.3066	0.2392	0.4017	0.0414	0.8673	-0.004	-0.0457	0.1462	-0.0037	0.0071	0.0279	-0.1527	-0.03	-0	0.4383	0.0112	0.0263	0.4007	-0.014	0.3173	59.1858	52.338	67.7748
17	0.1228	-0.0763	-0.0998	0.0661	-0.0386	0.1102	-0.0605	0.2147	0.6225	-0.1261	0.1494	0.3469	-0.8523	-0.1169	-0.0002	0.6685	-0.0408	0.0104	0.4081	-0.0453	0.5611	68.5009	69.3431	66.0251
18	0.1335	0.089	-0.0291	0.1272	-0.1067	0.1606	-0.3937	0.4057	0.7604	-0.9498	0.3853	0.0884	-0.9046	0.4984	-0.0045	0.8453	-0.0599	0.082	0.5585	0.0725	0.6017	69.5332	72.8934	57.8469
19	0.1094	0.0096	-0.1801	0.0745	-0.0118	0.1666	0.0652	0.0697	0.9297	-0.1161	-0.2718	0.1629	0.0159	-0.0743	0.0002	0.6146	-0.0752	0.0436	0.4975	0.0009	0.4756	73.5573	61.1423	58.1945
20	0.0786	0.0248	-0.0381	0.2909	-0.2272	0.0592	0.1356	0.3381	-0.1267	-0.6193	0.1932	-0.4186	-0.3279	0.1366	0.0001	0.7466	-0.0983	0.1621	0.8155	-0.084	0.5552	80.7154	61.937	55.1788
21	0.305	-0.0939	0.3362	0.9254	-0.3647	0.2219	-0.0501	-0.1883	0.1485	0.186	-0.0815	-0.2715	-0.1406	0.1417	-0	0.4962	-0.0232	0.0309	0.4564	-0.0718	0.3719	73.3967	54.5512	71.7543
22	0.5746	-0.1901	0.449	0.3161	0.1206	0.5009	-0.4757	-0.0493	0.0229	0.7253	-0.0624	0.2351	0.3645	0.2308	-0.0401	1.0138	0.1727	0.1524	0.6126	-0.0303	0.5833	25.1397	78.6301	44.9853
23	0.0352	0.0699	-0.023	0.0632	-0.041	0.0351	-0.1014	-0.1568	-0.1646	0.9988	0.1049	0.54	0.2823	-0.06	0.0019	1.2761	0.3338	-0.0775	0.885	-0.2228	0.6488	30.6685	79.0383	53.5138
24	1.3185	-0.1645	-0.3957	0.3044	-0.0715	0.1543	-0.2349	-0.0927	0.2075	0.2811	-0.2188	-0.098	-0.7005	0.0593	-0.4948	1.0345	0.142	-0.3316	0.4389	-0.0167	0.5798	40.947	71.631	55.6998
25	0.2188	0.3173	-0.1103	0.7089	-0.5948	0.884	-0.6237	0.4863	-0.1487	-0.999	-0.5605	-0.5485	-0.719	0.2262	-0.5455	1.4921	0.111	-0.3508	-0.06	0.6826	0.0272	48.9291	67.9905	52.7663

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:73)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 74:166)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 167:187)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 188:227)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 228:250)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 251:284)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 285:310)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 11:19)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 20:45)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 46:57)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 58:87)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 88:104)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 105:153)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 1:32)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 33:53)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 54:166)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 167:187)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 188:218)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 219:236)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 237:261)
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 262:310)
22	X-RAY DIFFRACTION	22	chain 'D' and (resseq 11:67)
23	X-RAY DIFFRACTION	23	chain 'D' and (resseq 68:87)
24	X-RAY DIFFRACTION	24	chain 'D' and (resseq 88:138)
25	X-RAY DIFFRACTION	25	chain 'D' and (resseq 139:153)

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