PDB-38yx: Crystal structure of Phosphoribosylaminoimidazole carboxylase fro...

ID or keywords:

Entry

Database: PDB / ID: 38yx

Title

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans in complex with aminoimidazole 4-carboxamide ribonucleotide

Components

N5-carboxyaminoimidazole ribonucleotide synthase

Keywords

LYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Phosphoribosylaminoimidazole carboxylase

Function / homology

Function and homology information

5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / metal ion binding / ATP binding / cytosol
Similarity search - Function

Biological species

Paraburkholderia xenovorans LB400 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.59 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To be published
Title: Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans in complex with aminoimidazole 4-carboxamide ribonucleotide
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Sep 24, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 7, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	38yx.cif.gz	574.3 KB	Display	PDBx/mmCIF format
PDB format	pdb38yx.ent.gz	474 KB	Display	PDB format
PDBx/mmJSON format	38yx.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/8y/38yx ftp://data.pdbj.org/pub/pdb/validation_reports/8y/38yx	HTTPS FTP

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Related structure data

Similar structure data	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 (4) #192 - Dec 2015 Vancomycin similarity (4) #154 - Oct 2012 Citric Acid Cycle similarity (3) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (4) #137 - May 2011 Cytochrome bc1 similarity (1)

Deposited unit

A: N5-carboxyaminoimidazole ribonucleotide synthase

B: N5-carboxyaminoimidazole ribonucleotide synthase

C: N5-carboxyaminoimidazole ribonucleotide synthase

D: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

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

1

A: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

defined by author
Evidence: gel filtration
42.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

defined by author
43 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

defined by author
43 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: N5-carboxyaminoimidazole ribonucleotide synthase

hetero molecules

defined by author
42.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.804, 170.975, 173.286
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	N5-carboxyaminoimidazole ribonucleotide synthase / N5-CAIR synthase / 5-(carboxyamino)imidazole ribonucleotide synthetase Mass: 42509.523 Da / Num. of mol.: 4 / Fragment: S9-T397 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paraburkholderia xenovorans LB400 (bacteria) Gene: purK, Bxe_A0694 / Plasmid: BuxeA.00036.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q13UJ9, 5-(carboxyamino)imidazole ribonucleotide synthase

#1: Protein

N5-carboxyaminoimidazole ribonucleotide synthase / N5-CAIR synthase / 5-(carboxyamino)imidazole ribonucleotide synthetase

Mass: 42509.523 Da / Num. of mol.: 4 / Fragment: S9-T397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Paraburkholderia xenovorans LB400 (bacteria)
Gene: purK, Bxe_A0694 / Plasmid: BuxeA.00036.a.B2 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q13UJ9, 5-(carboxyamino)imidazole ribonucleotide synthase

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Non-polymers , 5 types, 165 molecules

#2: Chemical	ChemComp-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR Mass: 338.211 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₅N₄O₈P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.91 Å³/Da / Density % sol: 57.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Berkeley E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME, Overnight soak in 10mM AMZ. plate 21242 A1, Puck: PSL-0411, Cryo: 100 mM sodium citrate ...Details: Berkeley E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME, Overnight soak in 10mM AMZ. plate 21242 A1, Puck: PSL-0411, Cryo: 100 mM sodium citrate tribasic/HCl pH 5.5, 200 mM sodium malonate dibasic pH 5.0, 33% PEG 2000 MME

Crystal

Density Matthews: 2.91 Å³/Da / Density % sol: 57.73 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Berkeley E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME, Overnight soak in 10mM AMZ. plate 21242 A1, Puck: PSL-0411, Cryo: 100 mM sodium citrate ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 26, 2026
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.59→47.86 Å / Num. obs: 62743 / % possible obs: 100 % / Redundancy: 13.6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.219 / R_pim(I) all: 0.061 / R_rim(I) all: 0.228 / Χ²: 1.07 / Net I/σ(I): 11.2 / Num. measured all: 853096
Reflection shell	Resolution: 2.59→2.66 Å / % possible obs: 100 % / Redundancy: 13.1 % / R_merge(I) obs: 1.775 / Num. measured all: 60210 / Num. unique obs: 4582 / CC_1/2: 0.678 / R_pim(I) all: 0.506 / R_rim(I) all: 1.847 / Χ²: 0.94 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(2.2_6143: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.59→47.61 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2377	3242	5.17 %
R_work	0.181	-	-
obs	0.1838	62659	99.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.59→47.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11276	0	90	150	11516

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	11638
X-RAY DIFFRACTION	f_angle_d	1.164	15899
X-RAY DIFFRACTION	f_dihedral_angle_d	14.422	4200
X-RAY DIFFRACTION	f_chiral_restr	0.061	1848
X-RAY DIFFRACTION	f_plane_restr	0.012	2112

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 (%)
2.59-2.63	0.4342	142	0.3551	2535	X-RAY DIFFRACTION	100
2.63-2.67	0.3198	132	0.3003	2593	X-RAY DIFFRACTION	100
2.67-2.71	0.3361	146	0.2717	2487	X-RAY DIFFRACTION	100
2.71-2.76	0.3353	170	0.2692	2543	X-RAY DIFFRACTION	100
2.76-2.81	0.3137	148	0.2409	2537	X-RAY DIFFRACTION	100
2.81-2.86	0.3443	125	0.2299	2573	X-RAY DIFFRACTION	100
2.86-2.92	0.293	143	0.2179	2536	X-RAY DIFFRACTION	100
2.92-2.99	0.2845	149	0.2167	2528	X-RAY DIFFRACTION	100
2.99-3.06	0.2877	145	0.2214	2578	X-RAY DIFFRACTION	100
3.06-3.13	0.2601	124	0.2412	2549	X-RAY DIFFRACTION	100
3.13-3.22	0.2871	158	0.2463	2559	X-RAY DIFFRACTION	100
3.22-3.31	0.308	153	0.2452	2533	X-RAY DIFFRACTION	100
3.31-3.42	0.2511	122	0.1809	2603	X-RAY DIFFRACTION	100
3.42-3.54	0.2181	122	0.1712	2599	X-RAY DIFFRACTION	100
3.54-3.68	0.2261	164	0.1656	2545	X-RAY DIFFRACTION	100
3.68-3.85	0.227	121	0.158	2594	X-RAY DIFFRACTION	100
3.85-4.05	0.206	129	0.1472	2600	X-RAY DIFFRACTION	100
4.05-4.31	0.1675	149	0.1293	2583	X-RAY DIFFRACTION	100
4.31-4.64	0.1631	153	0.1252	2590	X-RAY DIFFRACTION	100
4.64-5.11	0.1849	156	0.131	2616	X-RAY DIFFRACTION	100
5.11-5.84	0.2458	127	0.156	2633	X-RAY DIFFRACTION	100
5.84-7.36	0.23	121	0.1822	2706	X-RAY DIFFRACTION	100
7.36-47.61	0.2151	143	0.168	2797	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	0.5793	-0.0911	0.6745	0.0541	-0.0576	1.3995	0.0389	0.1612	-0.1242	-0.086	-0.0814	-0.1008	-0.1319	0.0953	0	0.4174	-0.0178	-0.0073	0.4593	-0.0265	0.3454	-5.7937	20.6529	-5.0187
2	0.2651	-0.3128	-0.2198	0.3665	0.2197	0.2798	0.3895	-0.3118	0.0554	-0.1766	-0.2333	-0.0831	-0.1585	-0.3321	-0.0003	0.4586	-0.0509	-0.0137	0.6048	-0.025	0.4726	-31.9888	12.614	-2.5101
3	1.3112	0.3704	0.9175	0.7369	0.8556	1.6726	-0.0112	-0.0241	-0.0912	0.0657	0.0597	-0.0868	0.1462	-0.129	-0.0151	0.3472	-0.012	-0.0275	0.3148	0.0535	0.3327	-10.5819	18.1246	12.9571
4	0.463	-0.0108	0.0007	0.076	-0.1482	0.1442	-0.1001	-0.221	0.3188	0.0993	0.006	0.2654	-0.06	-0.4301	-0	0.428	0.0498	-0.061	0.5498	0.0056	0.4742	-15.7275	29.069	19.7082
5	0.9281	0.6225	-0.1466	2.2071	-0.3642	0.4659	-0.0889	0.0271	0.1397	-0.3605	0.2061	0.2952	-0.0455	0.0004	0.259	0.49	-0.0492	-0.0514	0.2943	0.0388	0.393	11.6157	49.5676	19.1886
6	0.0411	-0.0144	-0.1273	0.2624	0.2573	0.6272	0.202	0.1681	-0.711	-0.1877	0.1099	-0.4516	-0.3822	0.1174	0.0469	0.4602	-0.0615	-0.0433	0.4934	-0.0571	0.5964	36.271	47.4713	31.362
7	0.7299	0.2287	0.2039	1.4837	0.3467	0.4377	-0.0158	0.0243	-0.1139	0.0502	0.006	0.0026	-0.0624	-0.0014	-0	0.3569	0.0004	-0.0374	0.3336	0.0226	0.3721	14.0662	32.2651	26.2019
8	0.5324	0.0616	0.263	0.1945	0.2286	0.3362	-0.0585	0.0159	-0.2395	0.0228	-0.0496	-0.2728	0.1155	0.0616	-0	0.3908	-0.0056	-0.0124	0.4462	0.0481	0.5081	19.8468	22.9236	17.4688
9	0.0701	-0.0658	-0.0207	0.0604	0.0047	0.1738	-0.1015	-0.1772	0.1054	0.2204	0.146	0.3002	-0.3662	0.0101	0.002	0.4249	0.0113	0.03	0.5433	0.1436	0.4939	10.7398	-3.7307	62.6337
10	0.5785	-0.4309	0.1191	0.2486	-0.1098	-0.0379	0.0213	0.1289	-0.2422	-0.0244	0.0176	0.0828	0.1528	-0.1878	0	0.395	0.0277	-0.0163	0.4444	0.1062	0.4303	24.2065	-17.922	56.8631
11	0.0631	0.0042	-0.0125	0.1651	-0.0674	0.2346	0.1582	-0.1781	0.3997	0.0899	0.0064	-0.1536	0.0664	0.1976	0	0.4141	0.0153	0.0624	0.454	0.0707	0.4369	46.1216	-14.5254	51.6903
12	0.6235	-0.8195	0.2221	1.4666	-0.3112	0.5837	-0.0041	0.0349	0.0283	-0.0789	-0.1634	-0.1262	0.1038	0.1019	-0.123	0.2886	-0.0029	-0.007	0.3956	0.1248	0.3264	24.3878	0.9752	46.4713
13	0.1254	0.0179	-0.0881	0.0979	-0.0322	0.1061	-0.0031	0.1783	0.1566	0.0093	-0.1699	-0.566	0.1207	0.4987	-0.005	0.4463	0.0162	-0.0645	0.5613	0.1862	0.5981	29.7053	13.1979	50.977
14	0.0444	-0.0269	-0.0692	0.133	0.0431	0.1125	-0.2039	-0.3273	-0.2642	0.1199	0.0719	-0.0951	0.0749	-0.2158	-0	0.547	0.038	0.0059	0.5522	0.0293	0.381	12.8733	17.2629	65.1552
15	0.1162	0.1718	0.0779	0.2444	0.092	0.3873	0.032	-0.5546	0.1013	0.841	-0.3537	0.1536	-0.0884	-0.1314	-0.0045	0.843	-0.018	0.1067	0.7046	-0.0623	0.4317	7.3829	19.6329	74.0483
16	0.1807	0.2376	0.0292	0.6642	0.1371	0.054	-0.2623	-0.4488	0.2297	0.8624	0.07	0.2397	-0.615	-0.8559	-0.1235	0.8498	0.22	0.2293	0.8128	-0.109	0.6178	-7.2603	37.0644	62.3296
17	1.0058	0.0516	0.7489	1.0836	0.2377	0.5645	0.1319	0.1648	-0.3049	0.2072	-0.0147	0.8565	-0.2864	-0.8555	0.2462	0.4423	0.3754	0.2328	1.3485	0.2783	1.0985	-24.0016	33.9379	59.4409
18	0.6387	-0.0605	0.2833	0.4763	-0.0609	0.8968	-0.0232	-0.067	-0.0153	0.1063	0.0368	0.1565	-0.1605	-0.0824	-0	0.391	0.0205	0.0132	0.379	0.0574	0.4354	-1.0891	21.0345	50.6996
19	0.1418	0.1054	-0.1655	0.0738	-0.0858	0.1051	0.1002	0.3595	0.0471	-0.2417	0.1257	0.4819	0.1161	-0.2602	0.0006	0.3506	-0.0346	0.0034	0.4702	0.1258	0.5458	-5.4761	7.9334	46.7266

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 143 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 144 through 195 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 196 through 357 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 358 through 396 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 9 through 143 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 144 through 195 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 196 through 357 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 358 through 397 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 8 through 59 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 60 through 143 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 144 through 195 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 196 through 357 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 358 through 396 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 8 through 35 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 36 through 97 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 98 through 143 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 144 through 182 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 183 through 357 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 358 through 397 )

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