PDB-5cvt: Structure of a single tryptophan mutant of Acetobacter aceti PurE...

Basic information

• Entry: Database: PDB / ID: 5cvt
• Title: Structure of a single tryptophan mutant of Acetobacter aceti PurE containing 5-fluorotryptophan, pH 5.4
• 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 / CITRIC ACID / : / 2,5,8,11-TETRAOXATRIDECANE / N5-carboxyaminoimidazole ribonucleotide mutase

• Biological species: Acetobacter aceti 1023 (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.78 Å
• Authors: Sullivan, K.L. / Kappock, T.J.
• 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	Jul 27, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2016	Provider: repository / Type: Initial release
Revision 1.1	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 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

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)	38,379	8
Polymers	37,645	2
Non-polymers	734	6
Water	4,648	258

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)	153,516	32
Polymers	150,581	8
Non-polymers	2,935	24
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	36100 Å2
ΔGint	-174 kcal/mol
Surface area	39040 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	98.695, 98.695, 165.057
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	A-415- 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: 18822.631 Da / Num. of mol.: 2 / Mutation: W34F,Y165F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti 1023 (bacteria) / Gene: purE, AZ09_02690 / Plasmid: pET23a / Details (production host): pJK698 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase

Non-polymers , 5 types, 264 molecules

#2: Chemical

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

Details:

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

#3: Chemical

A-201 B-201 ChemComp-CIT / CITRIC ACID / Citric acid

Details:

Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇

#4: Chemical

B-202 ChemComp-K / POTASSIUM ION

Details:

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

#5: Chemical

B-203 ChemComp-PGF / 2,5,8,11-TETRAOXATRIDECANE

Details:

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

#6: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION

Sample preparation

• Crystal: Density Matthews: 2.44 ų/Da / Density % sol: 49.6 %
• Crystal grow: Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4 ; Details: 21% (w/v) PEG 4000, 190 mM ammonium acetate, 90 mM sodium citrate

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
• Detector: Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2015
• Radiation: Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97872 Å / Relative weight: 1
• Reflection: Resolution: 1.78→50 Å / Num. obs: 39768 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.1 % / B_iso Wilson estimate: 22.15 Ų / R_sym value: 0.135 / Net I/σ(I): 37.46
• Reflection shell: Resolution: 1.78→1.82 Å / Redundancy: 13.7 % / R_merge(I) obs: 0.908 / Mean I/σ(I) obs: 2.6 / % possible all: 100

Processing

Software

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

Refinement

Method to determine structure: FOURIER SYNTHESIS
Starting model: 4ycb

4ycb

Resolution: 1.78→42.64 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18 / Stereochemistry target values: ML

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.1554	1557	3.96 %	same as 4ycb
Rwork	0.1428	-	-	-
obs	0.1434	39358	99.94 %	-

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

Refinement step

Cycle: LAST / Resolution: 1.78→42.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2321	0	48	258	2627

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2522
X-RAY DIFFRACTION	f_angle_d	1.204	3461
X-RAY DIFFRACTION	f_dihedral_angle_d	13.654	938
X-RAY DIFFRACTION	f_chiral_restr	0.051	415
X-RAY DIFFRACTION	f_plane_restr	0.006	452

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.7801-1.8375	0.2007	45	0.1953	3499	X-RAY DIFFRACTION	100
1.8375-1.9032	0.3323	3	0.1752	3507	X-RAY DIFFRACTION	100
1.9032-1.9794	0.186	78	0.172	3441	X-RAY DIFFRACTION	100
1.9794-2.0695	0.1657	183	0.1537	3340	X-RAY DIFFRACTION	100
2.0695-2.1786	0.1637	176	0.1455	3366	X-RAY DIFFRACTION	100
2.1786-2.3151	0.1681	193	0.1495	3344	X-RAY DIFFRACTION	100
2.3151-2.4938	0.1589	179	0.1442	3395	X-RAY DIFFRACTION	100
2.4938-2.7447	0.185	167	0.1425	3413	X-RAY DIFFRACTION	100
2.7447-3.1418	0.1708	186	0.1466	3394	X-RAY DIFFRACTION	100
3.1418-3.9578	0.1354	173	0.1278	3482	X-RAY DIFFRACTION	100
3.9578-42.6518	0.139	174	0.1319	3620	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	2.7886	-1.3471	0.202	0.6975	-0.5832	5.0494	0.0951	-0.3603	0.4663	0.5261	-0.0997	0.0406	-0.3811	0.0988	0.0847	0.2244	0.004	-0.0083	0.2217	-0.0772	0.2747	-6.0831	30.2255	35.5176
2	8.5454	5.7026	-0.0922	4.5766	-0.2549	4.8443	0.2158	-0.6633	0.0999	0.4196	-0.2891	-0.0729	0.1234	0.1147	0.0505	0.1713	0.0181	-0.0186	0.1868	-0.036	0.1407	-1.0057	22.9914	40.9357
3	3.8926	3.7716	2.6815	5.1732	2.435	2.4613	0.0591	-0.2103	0.1895	0.2319	-0.1131	-0.0612	0.08	-0.0928	0.0843	0.1859	-0.0051	0.0095	0.1576	-0.0544	0.1727	-8.2578	27.5455	36.0535
4	9.2177	7.8875	-5.5246	7.3406	-4.6815	4.434	0.0403	0.1503	0.662	0.118	0.0791	0.4483	-0.2802	-0.1049	-0.1368	0.1888	0.0479	-0.0075	0.1803	-0.0512	0.2856	-16.6522	30.1922	28.5871
5	1.9765	-0.345	0.467	2.561	-0.3099	2.9334	-0.0208	-0.0012	0.2305	-0.0796	-0.0364	0.0123	-0.1285	-0.047	0.0474	0.133	-0.003	0.0003	0.1164	-0.0191	0.1872	-7.6993	26.5501	26.7677
6	2.0621	-2.198	-1.4331	5.2782	-0.52	2.4265	0.1113	-0.8488	-0.78	1.1465	-0.278	-0.4344	0.6911	-0.2218	0.2686	0.3709	-0.0697	-0.0212	0.3144	0.0758	0.2844	-4.7047	5.7928	34.5742
7	2.1752	1.0003	0.4219	2.0786	0.4333	1.9455	-0.0671	0.0082	0.1458	-0.0335	0.0214	0.067	-0.0965	-0.0166	0.0421	0.089	0.0042	-0.0034	0.1093	-0.0141	0.1359	0.6935	22.1942	26.0917
8	4.4162	-5.0782	4.4157	7.1135	-3.9519	5.4066	0.0581	0.0696	-0.0114	-0.1185	-0.0063	-0.0291	-0.0024	0.277	-0.0687	0.1772	-0.0438	-0.0264	0.1972	-0.0255	0.2411	15.0127	32.0147	34.8999
9	5.8736	-5.5803	1.5232	5.7773	-0.3752	2.8507	-0.0698	-0.7158	-0.6168	1.1424	0.4112	0.0573	0.6437	0.1841	-0.3677	0.4474	0.0102	-0.0749	0.3388	-0.0076	0.3218	24.2913	14.0933	43.4372
10	4.2463	0.2364	-0.224	0.1043	0.6457	4.7656	0.0468	0.1216	0.3453	-0.3985	0.014	-0.0488	-0.2551	0.1897	-0.008	0.1487	-0.0253	-0.0078	0.1562	0.0399	0.1619	13.1946	28.2566	11.5424
11	7.8497	-5.7529	-1.8362	8.822	1.5026	5.3477	0.1701	0.3905	-0.1409	-0.4494	-0.2041	0.2798	0.0161	-0.3676	0.0547	0.1772	-0.0342	-0.0421	0.2013	0.0196	0.1344	6.6412	22.4654	6.0183
12	1.6863	-0.2695	-0.0491	0.4765	-0.0904	1.523	0.0164	0.0178	0.1619	-0.0326	-0.0461	-0.1037	-0.0568	0.162	0.0336	0.173	-0.0155	-0.0168	0.1503	0.0063	0.1949	15.9155	24.7008	17.5099
13	1.847	-0.4499	-1.9567	0.3809	0.6167	4.9392	0.1629	0.5626	-0.5307	-1.4853	-0.3803	0.8987	0.3129	-0.1647	0.2871	0.4395	0.0457	-0.0652	0.2684	-0.0423	0.3091	6.0274	4.6417	12.0222
14	1.5785	-1.0717	0.193	3.7167	-0.4443	2.1988	-0.0327	-0.0194	0.0669	-0.0243	0.0318	0.0331	-0.066	0.0145	0.0053	0.0929	-0.0193	-0.0002	0.1409	0.0004	0.1589	4.2857	21.866	20.3756
15	7.624	4.8023	3.9422	3.3919	3.3562	4.216	-0.0774	-0.0693	0.3852	0.0285	0.0343	0.2474	-0.2375	-0.1332	-0.0148	0.2702	0.0177	-0.0577	0.1774	0.04	0.2904	-7.2182	35.3351	12.2254
16	8.8509	6.4363	6.0104	4.7388	4.3493	4.1517	-0.127	0.2294	-0.1986	-0.5234	0.2104	-0.1137	-0.2209	0.2745	-0.1826	0.3314	-0.002	-0.0091	0.2423	0.0202	0.2367	-20.4603	17.645	1.7786

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 20 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 180 )
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 181 )