PDB-9zoi: Crystal structure of Phosphoribosylaminoimidazole carboxylase fro...

ID or keywords:

Entry

Database: PDB / ID: 9zoi

Title

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ATP complex)

Components

N5-carboxyaminoimidazole ribonucleotide synthase

Keywords

LYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / TRANSFERASE / 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 / ATP binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Paraburkholderia xenovorans LB400 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans (ATP complex)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Dec 15, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9zoi.cif.gz	600.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9zoi.ent.gz	493.2 KB	Display	PDB format
PDBx/mmJSON format	9zoi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9zoi_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	9zoi_full_validation.pdf.gz	1.7 MB	Display
Data in XML	9zoi_validation.xml.gz	71.9 KB	Display
Data in CIF	9zoi_validation.cif.gz	95.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zo/9zoi ftp://data.pdbj.org/pub/pdb/validation_reports/zo/9zoi	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

173 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
43.2 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
43.4 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
43.2 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
43.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	67.007, 170.436, 170.508
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 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
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 , 8 types, 749 molecules

#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#8: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 730 / 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: 2.86 Å³/Da / Density % sol: 57.04 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP, plate 20558 E6 drop 1, Puck: ...Details: BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP, plate 20558 E6 drop 1, Puck: PSL-1913, Cryo: 20% PEG 200 + 80% crystallant

Crystal

Density Matthews: 2.86 Å³/Da / Density % sol: 57.04 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: BRK E6: 100 mM sodium citrate, pH 5.5, 200 mM sodium malonate, pH 5.0, 20% PEG 2000 MME. BuxeA.00036.a.B2.PW39468 at 23.8 mg/mL. Cocrystallization with 3mM ATP, plate 20558 E6 drop 1, Puck: ...

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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: Nov 10, 2025
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: 1.93→47.28 Å / Num. obs: 146557 / % possible obs: 99.5 % / Redundancy: 13.7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.146 / R_pim(I) all: 0.041 / R_rim(I) all: 0.151 / Χ²: 1.27 / Net I/σ(I): 15 / Num. measured all: 2005611
Reflection shell	Resolution: 1.93→1.98 Å / % possible obs: 98.8 % / Redundancy: 14.4 % / R_merge(I) obs: 1.957 / Num. measured all: 152668 / Num. unique obs: 10626 / CC_1/2: 0.759 / R_pim(I) all: 0.53 / R_rim(I) all: 2.028 / Χ²: 0.95 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5765: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.93→44.81 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1956	7285	4.98 %
R_work	0.1691	-	-
obs	0.1704	146422	99.44 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.93→44.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11473	0	185	730	12388

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	12028
X-RAY DIFFRACTION	f_angle_d	1.033	16415
X-RAY DIFFRACTION	f_dihedral_angle_d	13.008	4433
X-RAY DIFFRACTION	f_chiral_restr	0.06	1881
X-RAY DIFFRACTION	f_plane_restr	0.009	2154

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 (%)
1.93-1.95	0.3323	196	0.318	4653	X-RAY DIFFRACTION	100
1.95-1.97	0.3238	214	0.2925	4535	X-RAY DIFFRACTION	97
1.97-2	0.2811	239	0.2594	4570	X-RAY DIFFRACTION	100
2-2.02	0.2811	259	0.2456	4527	X-RAY DIFFRACTION	98
2.02-2.05	0.2538	222	0.2326	4587	X-RAY DIFFRACTION	99
2.05-2.08	0.251	273	0.2256	4580	X-RAY DIFFRACTION	100
2.08-2.11	0.255	231	0.216	4540	X-RAY DIFFRACTION	98
2.11-2.14	0.2433	189	0.2022	4642	X-RAY DIFFRACTION	100
2.14-2.17	0.2272	238	0.1933	4559	X-RAY DIFFRACTION	98
2.17-2.21	0.2129	276	0.1923	4574	X-RAY DIFFRACTION	100
2.21-2.25	0.2493	248	0.1938	4531	X-RAY DIFFRACTION	98
2.25-2.29	0.2354	242	0.1871	4635	X-RAY DIFFRACTION	100
2.29-2.33	0.2219	255	0.1852	4591	X-RAY DIFFRACTION	99
2.33-2.38	0.2276	220	0.1713	4642	X-RAY DIFFRACTION	100
2.38-2.43	0.1913	228	0.1678	4562	X-RAY DIFFRACTION	99
2.43-2.49	0.1936	224	0.1628	4668	X-RAY DIFFRACTION	99
2.49-2.55	0.2253	227	0.1653	4641	X-RAY DIFFRACTION	100
2.55-2.62	0.2386	234	0.161	4614	X-RAY DIFFRACTION	99
2.62-2.7	0.1912	225	0.1617	4661	X-RAY DIFFRACTION	100
2.7-2.78	0.1954	244	0.1724	4682	X-RAY DIFFRACTION	100
2.78-2.88	0.2184	232	0.1806	4603	X-RAY DIFFRACTION	100
2.88-3	0.2137	258	0.1889	4655	X-RAY DIFFRACTION	100
3-3.13	0.2048	254	0.183	4654	X-RAY DIFFRACTION	100
3.13-3.3	0.2012	242	0.1763	4675	X-RAY DIFFRACTION	100
3.3-3.51	0.1938	266	0.1716	4671	X-RAY DIFFRACTION	100
3.51-3.78	0.1796	267	0.1541	4686	X-RAY DIFFRACTION	100
3.78-4.16	0.1814	279	0.135	4717	X-RAY DIFFRACTION	100
4.16-4.76	0.1399	278	0.1173	4713	X-RAY DIFFRACTION	100
4.76-5.99	0.1565	255	0.1402	4797	X-RAY DIFFRACTION	100
5.99-44.81	0.176	270	0.1733	4972	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	0.6873	-0.1401	0.1824	1.1889	0.3216	0.3264	-0.0145	0.0804	0.1288	0.207	0.0254	-0.1014	0.0311	0.1823	0	0.2901	0.0021	0.0002	0.292	-0.0201	0.296	-16.2124	47.1174	-15.5294
2	0.212	0.0617	-0.113	0.0766	0.1603	0.1279	0.1966	0.3513	0.3134	-0.1546	-0.1704	-0.0691	-0.0435	0.1343	0	0.3531	0.0292	-0.0058	0.3604	0.0392	0.3226	-33.9869	47.9693	-34.5436
3	0.484	-0.2178	-0.2997	0.7492	0.1423	0.5389	0.1382	-0.0033	-0.0442	0.0437	-0.0301	0.1809	-0.0258	-0.1047	0	0.2832	0.0261	-0.0252	0.3144	0.0053	0.2983	-48.1351	44.7235	-29.5232
4	1.0924	-0.1596	0.1285	1.2227	-0.3377	0.547	0.076	0.2063	-0.0696	-0.145	-0.0744	0.0836	0.0558	0.0114	-0	0.2665	0.039	-0.0095	0.2917	-0.0413	0.2379	-25.9048	30.6105	-28.3824
5	0.9097	0.0766	-0.0488	0.5932	-0.4701	0.4767	0.0283	-0.064	-0.0773	0.0841	0.0399	0.2714	0.0077	-0.2121	-0	0.2997	0.0138	0.027	0.3348	-0.027	0.3392	-32.8644	23.6087	-9.2085
6	0.2497	-0.3576	0.2394	0.4735	0.0057	0.64	-0.0278	0.0531	0.1274	0.0434	0.0087	0.0492	-0.2092	0.0422	0	0.3562	0.0233	-0.0157	0.3456	-0.0306	0.3262	-12.0135	31.708	0.5034
7	0.6486	0.0441	0.5365	-0.0043	-0.1471	1.3081	-0.0061	0.0278	-0.0456	0.1205	-0.0255	0.0054	-0.0052	0.0817	-0	0.3041	-0.015	-0.013	0.3019	-0.0008	0.2713	2.5068	16.9818	10.2702
8	0.3687	0.3525	-0.269	0.359	-0.1693	0.4509	0.0931	0.8573	0.4223	-0.2066	-0.1589	-0.2334	-0.4003	0.6109	0.0055	0.3444	-0.0697	-0.0309	0.7052	0.0873	0.3393	22.6529	13.2748	5.5591
9	0.1252	-0.1564	0.4237	0.5601	-0.2796	0.337	0.1052	0.0418	-0.0833	0.0273	-0.0993	-0.1222	0.1678	0.1967	-0	0.2877	0.0224	-0.0069	0.3805	-0.0315	0.2733	3.2355	10.4688	-4.0799
10	0.4922	0.0397	-0.0323	0.5553	-0.2158	0.5312	0.0364	0.0446	0.0202	-0.0024	-0.0296	-0.0383	0.0694	0.0733	0	0.2683	0.028	-0.0033	0.2978	-0.0255	0.2532	-2.36	17.6378	-10.4345
11	0.8778	0.0462	-0.1601	0.2733	-0.3007	0.3751	0.1005	0.025	-0.1148	-0.0563	0.0592	-0.2516	0.1292	0.3699	-0	0.2753	0.031	0.0212	0.3687	-0.0525	0.3154	3.3729	25.0789	-19.6452
12	0.5833	0.4966	-0.2228	0.8509	0.3177	0.6959	0.0058	0.0967	-0.2216	0.1322	-0.146	0.0001	0.2597	-0.0955	-0	0.3576	-0.0168	0.026	0.3283	-0.0771	0.3677	-3.823	-20.3998	-50.8287
13	0.9201	-0.3421	-0.6275	0.1702	0.1276	0.7591	0.0267	-0.0741	0.1763	-0.0492	0.0351	-0.0281	-0.109	0.0843	-0	0.3133	-0.0223	0.0121	0.2996	-0.0788	0.3317	13.4409	-3.898	-50.1373
14	0.5585	0.0778	-0.103	0.2644	-0.2756	0.7672	-0.0827	-0.2072	0.0676	0.1105	0.0695	-0.1522	0.0483	0.5842	0.0037	0.321	0.091	-0.0259	0.5496	-0.1437	0.4012	13.0212	-11.6041	-26.536
15	0.1426	-0.051	-0.1924	0.1264	0.0445	0.1858	0.3093	0.2881	-0.025	-0.4629	-0.1774	0.056	0.3663	-0.0368	0	0.5689	0.067	0.0217	0.3629	-0.0536	0.4652	-3.89	-22.7935	-24.8505
16	0.9698	-0.5327	0.4912	1.0504	-0.1563	0.6384	0.0445	-0.2527	-0.3709	0.0851	-0.0004	0.2877	0.7257	-0.1331	0.0414	0.7042	-0.0614	-0.0336	0.3261	0.0007	0.5359	-11.9272	-28.4771	-18.051
17	0.191	-0.1709	0.1163	0.1701	-0.1361	0.2024	-0.0132	-0.2409	0.1424	0.4991	0.1441	1.1949	0.3278	-0.8477	0.0624	0.5058	-0.1919	0.1722	1.0332	0.0307	1.0113	-38.1297	-17.7428	-5.3543
18	0.3883	-0.0695	0.0385	1.115	0.1939	0.9223	-0.0193	-0.1163	-0.0875	0.1279	-0.091	0.2546	0.0715	-0.4435	-0	0.3465	0.0071	0.0106	0.4552	-0.0942	0.3744	-19.4457	-7.7946	-13.8332
19	0.2467	-0.0764	-0.1623	0.4053	-0.1495	0.4249	0.0395	0.0448	-0.1064	0.0397	0.002	0.0178	0.1598	-0.0867	-0	0.3148	0.0237	-0.0072	0.365	-0.0886	0.3326	-15.66	-9.1672	-31.8114
20	0.4763	-0.1617	0.377	0.1322	-0.0877	0.2112	-0.0359	-0.0879	0.1116	-0.063	0.0261	0.3683	-0.0082	-0.354	0	0.3409	0.0089	-0.0233	0.4355	-0.1022	0.4181	-22.1836	-4.5514	-34.4069

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 96 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 97 through 143 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 144 through 195 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 196 through 330 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 331 through 397 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 8 through 59 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 60 through 157 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 158 through 183 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 184 through 225 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 226 through 357 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 358 through 397 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 8 through 96 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 97 through 330 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 331 through 396 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 8 through 35 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 36 through 123 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 124 through 182 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 183 through 293 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 294 through 357 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 358 through 397 )

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Protein , 1 types, 4 molecules ABCD

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Sample preparation

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