PDB-4ycb: Structure of a single tryptophan mutant of Acetobacter aceti PurE

Basic information

• Entry: Database: PDB / ID: 4ycb
• Title: Structure of a single tryptophan mutant of Acetobacter aceti PurE
• Components: N5-carboxyaminoimidazole ribonucleotide mutase
• Keywords: ISOMERASE / acidophile / PurE / purine biosynthesis

Function / homology

Function:

5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process

Domain/homology:

: / Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

ACETATE ION / : / 2,5,8,11-TETRAOXATRIDECANE / N5-carboxyaminoimidazole ribonucleotide mutase

• Biological species: Acetobacter aceti 1023 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
• Authors: Kappock, T.J. / Sullivan, K.L. / Mullins, E.A.
• Citation: Journal: To Be Published; Title: Structure of a single tryptophan mutant of Acetobacter aceti PurE; Authors: Sullivan, K.L. / Tranchimand, S. / Kappock, T.J.

History

Deposition	Feb 19, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 24, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 1, 2016	Group: Other
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

Assembly

Deposited unit

A: N5-carboxyaminoimidazole ribonucleotide mutase

B: N5-carboxyaminoimidazole ribonucleotide mutase

hetero molecules

Summary:

• 38.4 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,399	12
Polymers	37,609	2
Non-polymers	790	10
Water	7,080	393

1

A: N5-carboxyaminoimidazole ribonucleotide mutase

B: N5-carboxyaminoimidazole ribonucleotide mutase

hetero molecules

A: N5-carboxyaminoimidazole ribonucleotide mutase

B: N5-carboxyaminoimidazole ribonucleotide mutase

hetero molecules

A: N5-carboxyaminoimidazole ribonucleotide mutase

B: N5-carboxyaminoimidazole ribonucleotide mutase

hetero molecules

A: N5-carboxyaminoimidazole ribonucleotide mutase

B: N5-carboxyaminoimidazole ribonucleotide mutase

hetero molecules

Summary:

• defined by author&software
• 154 kDa, 8 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	153,596	48
Polymers	150,437	8
Non-polymers	3,159	40
Water	144	8

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1
crystal symmetry operation	3_555	-y,x,z	1
crystal symmetry operation	4_555	y,-x,z	1

Calculated values:

Buried area	35960 Å2
ΔGint	-176 kcal/mol
Surface area	42960 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	99.803, 99.803, 164.409
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	B-205- SO4
2	1	A-306- HOH
3	1	A-477- HOH
4	1	A-497- HOH
5	1	B-480- HOH

Components

Protein , 1 types, 2 molecules A B

#1: Protein

A B N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase

Details:

Mass: 18804.639 Da / Num. of mol.: 2 / Mutation: W34F, W165F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti 1023 (bacteria) / Gene: purE, AZ09_02690 / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase

Non-polymers , 6 types, 403 molecules

#2: Chemical

A-200 B-200 ChemComp-ACT / ACETATE ION

Details:

Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂

#3: Chemical

A-201 A-202 B-201 B-202
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Chemical

A-203 B-205 ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄

#5: Chemical

B-203 ChemComp-K / POTASSIUM ION

Details:

Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

#6: Chemical

B-204 ChemComp-PGF / 2,5,8,11-TETRAOXATRIDECANE

Details:

Mass: 192.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₂₀O₄

#7: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 2.72 ų/Da / Density % sol: 54.8 %
• Crystal grow: Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3 ; Details: 30% (w/v) PEG 4000, 0.1 M Tris-HCL, 0.2 M lithium sulfate

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
• Detector: Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 22, 2009
• Radiation: Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97856 Å / Relative weight: 1
• Reflection: Resolution: 1.35→50 Å / Num. all: 90070 / Num. obs: 90070 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.7 % / B_iso Wilson estimate: 12.12 Ų / R_merge(I) obs: 0.056 / R_sym value: 0.071 / Net I/σ(I): 48.1
• Reflection shell: Resolution: 1.35→1.37 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.461 / Mean I/σ(I) obs: 2 / % possible all: 87.5

Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fw1

2fw1

Resolution: 1.35→31.56 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.37 / Stereochemistry target values: ML

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.1492	3547	3.94 %	same as 2fw1
Rwork	0.1401	-	-	-
obs	0.1405	89999	99.22 %	-

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

Refinement step

Cycle: LAST / Resolution: 1.35→31.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2323	0	48	393	2764

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2640
X-RAY DIFFRACTION	f_angle_d	1.128	3625
X-RAY DIFFRACTION	f_dihedral_angle_d	12.117	1011
X-RAY DIFFRACTION	f_chiral_restr	0.043	430
X-RAY DIFFRACTION	f_plane_restr	0.006	472

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.35-1.3685	0.259	125	0.2339	2983	X-RAY DIFFRACTION	86
1.3685-1.388	0.2172	132	0.2097	3268	X-RAY DIFFRACTION	96
1.388-1.4088	0.1967	139	0.1893	3413	X-RAY DIFFRACTION	99
1.4088-1.4308	0.1835	140	0.1773	3411	X-RAY DIFFRACTION	100
1.4308-1.4542	0.1566	141	0.1617	3445	X-RAY DIFFRACTION	100
1.4542-1.4793	0.1775	142	0.1535	3462	X-RAY DIFFRACTION	100
1.4793-1.5062	0.1695	142	0.1446	3458	X-RAY DIFFRACTION	100
1.5062-1.5352	0.1599	142	0.1382	3459	X-RAY DIFFRACTION	100
1.5352-1.5665	0.1454	144	0.136	3445	X-RAY DIFFRACTION	100
1.5665-1.6006	0.1599	137	0.137	3448	X-RAY DIFFRACTION	100
1.6006-1.6378	0.1624	144	0.1355	3453	X-RAY DIFFRACTION	100
1.6378-1.6788	0.1337	142	0.1278	3472	X-RAY DIFFRACTION	100
1.6788-1.7241	0.1549	140	0.135	3462	X-RAY DIFFRACTION	100
1.7241-1.7749	0.172	145	0.1327	3478	X-RAY DIFFRACTION	100
1.7749-1.8322	0.1847	80	0.1367	3537	X-RAY DIFFRACTION	100
1.8322-1.8976	0.1407	2	0.1349	3592	X-RAY DIFFRACTION	100
1.8976-1.9736	0.1465	35	0.135	3599	X-RAY DIFFRACTION	100
1.9736-2.0634	0.1464	197	0.1344	3405	X-RAY DIFFRACTION	100
2.0634-2.1722	0.1386	169	0.1324	3496	X-RAY DIFFRACTION	100
2.1722-2.3082	0.1315	211	0.1345	3435	X-RAY DIFFRACTION	100
2.3082-2.4864	0.1473	177	0.1386	3454	X-RAY DIFFRACTION	100
2.4864-2.7365	0.1673	169	0.1433	3506	X-RAY DIFFRACTION	100
2.7365-3.1321	0.1812	194	0.147	3493	X-RAY DIFFRACTION	100
3.1321-3.945	0.1215	180	0.1298	3553	X-RAY DIFFRACTION	100
3.945-31.5691	0.1293	178	0.1359	3725	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	1.1941	-0.7333	0.0354	1.3564	-1.9683	4.1688	0.0316	-0.2273	0.2721	0.188	0.0466	0.1975	-0.0409	-0.098	-0.0703	0.113	0.013	-0.0024	0.1228	-0.0553	0.1453	-6.342	29.095	35.1745
2	7.2116	6.8503	-0.1755	9.0221	-0.2499	1.0032	0.1688	-0.5407	0.0219	0.3254	-0.2655	-0.085	0.0128	-0.0121	0.0842	0.151	-0.0045	-0.0117	0.1771	-0.0278	0.0968	-0.5414	23.4857	41.0331
3	6.7516	3.5601	0.8478	2.4803	0.4318	0.1113	0.0913	-0.2867	0.26	0.2418	-0.1159	0.0319	0.0302	-0.016	0.0248	0.1431	0.005	-0.0118	0.1456	-0.0525	0.1191	-8.2136	27.6328	36.0607
4	6.717	5.3782	-3	7.7532	-2.925	1.4753	-0.0603	0.0349	0.4758	-0.0162	0.0978	0.3167	-0.0299	-0.1128	-0.0326	0.101	0.0246	-0.014	0.1021	-0.0424	0.1433	-16.6309	30.4989	28.1704
5	1.4423	-0.1073	0.3188	1.0228	0.3812	1.15	-0.0352	-0.0496	0.229	-0.0862	-0.0443	0.0564	-0.1028	-0.0671	0.0595	0.0995	0.0064	-0.0135	0.0855	-0.0233	0.1232	-8.0226	26.8635	26.7846
6	2.0416	-1.261	-0.4683	7.2681	-0.1155	4.7566	0.1027	-0.4199	-0.3546	0.7665	-0.1221	-0.315	0.2283	0.0465	0.0906	0.1816	-0.026	-0.0237	0.1584	0.0364	0.1355	-4.474	5.8502	34.5125
7	1.4653	0.9818	0.4026	1.9377	0.3064	1.0662	0.0024	-0.0559	0.0699	0.0602	-0.0334	-0.0023	-0.0647	0.0028	0.0276	0.0721	0.0081	-0.0012	0.0776	-0.0143	0.0791	1.1183	22.0168	26.6405
8	4.3185	-3.7108	2.0689	5.7994	-1.4961	2.0519	0.0084	0.0453	0.117	-0.1019	0.0123	-0.0163	-0.0702	0.0482	-0.0223	0.123	-0.0289	-0.0328	0.1242	-0.0262	0.1217	15.3646	32.2029	34.6586
9	7.8116	-4.9223	2.9532	4.3846	-3.7001	6.2981	-0.0921	-0.4164	-0.4026	0.7131	0.1448	0.0135	0.4791	0.1885	-0.0736	0.2916	0.0274	-0.0595	0.1844	-0.0147	0.1444	24.267	14.5258	43.2396
10	3.9091	-0.3645	-0.2196	0.4665	1.1255	2.8315	0.0196	0.179	0.2559	-0.2623	-0.0199	0.0035	-0.2397	0.0501	0.0472	0.1387	-0.0315	-0.0078	0.117	0.0317	0.0936	13.2399	28.1796	11.4794
11	2.6197	-2.1506	-2.4155	2.5349	2.5834	2.8766	0.0346	0.2415	0.1032	-0.3027	-0.0961	0.1296	-0.1709	-0.1789	0.0547	0.148	-0.0177	-0.0375	0.1386	0.0199	0.1144	6.4608	22.5935	5.8934
12	1.11	-0.0635	-0.0978	1.1266	-0.1798	0.7608	-0.0103	0.0251	0.133	0.0017	-0.0183	-0.0623	-0.1135	0.0918	0.0347	0.1183	-0.022	-0.0171	0.0933	0.0066	0.1005	16.5018	24.5646	17.5781
13	3.1224	2.0592	1.5155	2.6097	-1.2798	4.894	0.007	0.3871	-0.2498	-0.6773	-0.0074	0.2549	0.2945	0.047	0.0599	0.1922	0.0129	-0.0265	0.1469	-0.0291	0.1512	5.7616	4.6986	12.1904
14	1.1851	-0.6681	0.114	2.2944	-0.2187	1.2018	-0.0163	0.0023	0.091	-0.0126	0.0113	-0.0105	-0.0873	0.0088	0.0018	0.0657	-0.0122	-0.0038	0.0761	-0.0031	0.0761	4.4186	21.7709	20.4677
15	8.9322	7.198	1.665	6.1551	1.0138	0.8853	-0.0482	0.13	0.4768	0.0907	0.0435	0.308	-0.1726	-0.0746	0.0392	0.1984	0.0407	-0.0381	0.1149	0.0325	0.1916	-7.3423	34.9176	11.9903
16	5.1917	2.5642	2.5962	5.8015	2.9154	7.7542	-0.2055	0.2517	-0.2627	-0.2855	0.1434	0.004	0.2717	0.0635	0.0842	0.1533	0.0027	0.0176	0.1424	0.0227	0.1209	-20.3929	16.266	0.5716

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 30 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 31 through 46 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 61 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 62 through 72 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 73 through 107 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 108 through 114 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 115 through 154 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 155 through 171 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 172 through 179 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 20 through 30 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 31 through 46 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 47 through 107 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 114 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 115 through 154 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 155 through 171 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 172 through 182 )