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

ID or keywords:

Entry

Database: PDB / ID: 38yy

Title

Crystal structure of Phosphoribosylaminoimidazole carboxylase from Burkholderia xenovorans in complex with 5'-sulfamoyladenosine

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: 2.79 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 5'-sulfamoyladenosine
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

-
Download

PDBx/mmCIF format	38yy.cif.gz	572.7 KB	Display	PDBx/mmCIF format
PDB format	pdb38yy.ent.gz	471.2 KB	Display	PDB format
PDBx/mmJSON format	38yy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/8y/38yy ftp://data.pdbj.org/pub/pdb/validation_reports/8y/38yy	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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
43 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
43.2 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
43.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	66.939, 171.320, 173.667
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
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

-
Non-polymers , 5 types, 74 molecules

#2: Chemical	ChemComp-LMS / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE Type: RNA linking / Mass: 346.320 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₆O₆S / 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.: 13 / 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.: 51 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 57.99 %
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 5'-O-sulfamoyladenosine. Puck: PSL-0413, 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 5'-O-sulfamoyladenosine. Puck: PSL-0413, 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: 2.93 Å³/Da / Density % sol: 57.99 %

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 5'-O-sulfamoyladenosine. Puck: PSL-0413, Cryo: 100 mM sodium citrate ...

-
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: 2.79→47.96 Å / Num. obs: 50681 / % possible obs: 100 % / Redundancy: 13.5 % / CC_1/2: 0.994 / R_merge(I) obs: 0.292 / R_pim(I) all: 0.082 / R_rim(I) all: 0.304 / Χ²: 1.1 / Net I/σ(I): 9.3 / Num. measured all: 686655
Reflection shell	Resolution: 2.79→2.86 Å / % possible obs: 100 % / Redundancy: 14.3 % / R_merge(I) obs: 1.843 / Num. measured all: 52308 / Num. unique obs: 3662 / CC_1/2: 0.73 / R_pim(I) all: 0.504 / R_rim(I) all: 1.911 / Χ²: 0.95 / Net I/σ(I) obs: 1.7

-
Processing

Software

Name	Version	Classification
PHENIX	(2.2.1_6174: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.79→47.71 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2437	2541	5.02 %
R_work	0.1893	-	-
obs	0.1919	50612	99.99 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.79→47.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11233	0	123	51	11407

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	11611
X-RAY DIFFRACTION	f_angle_d	0.769	15861
X-RAY DIFFRACTION	f_dihedral_angle_d	16.478	4125
X-RAY DIFFRACTION	f_chiral_restr	0.051	1844
X-RAY DIFFRACTION	f_plane_restr	0.007	2100

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 (%)
2.79-2.84	0.3962	137	0.3256	2602	X-RAY DIFFRACTION	100
2.84-2.9	0.3583	147	0.2933	2659	X-RAY DIFFRACTION	100
2.9-2.96	0.2921	142	0.2498	2595	X-RAY DIFFRACTION	100
2.96-3.03	0.3248	152	0.238	2636	X-RAY DIFFRACTION	100
3.03-3.11	0.293	134	0.2381	2612	X-RAY DIFFRACTION	100
3.11-3.19	0.3013	157	0.2416	2654	X-RAY DIFFRACTION	100
3.19-3.29	0.2939	130	0.2495	2642	X-RAY DIFFRACTION	100
3.29-3.39	0.3095	134	0.2281	2652	X-RAY DIFFRACTION	100
3.39-3.51	0.2925	152	0.1907	2651	X-RAY DIFFRACTION	100
3.51-3.66	0.2505	138	0.1826	2630	X-RAY DIFFRACTION	100
3.66-3.82	0.2617	149	0.1879	2642	X-RAY DIFFRACTION	100
3.82-4.02	0.2379	133	0.1688	2680	X-RAY DIFFRACTION	100
4.02-4.28	0.1794	140	0.1536	2683	X-RAY DIFFRACTION	100
4.28-4.61	0.1707	154	0.1362	2655	X-RAY DIFFRACTION	100
4.61-5.07	0.1873	122	0.1401	2721	X-RAY DIFFRACTION	100
5.07-5.8	0.2091	128	0.1688	2723	X-RAY DIFFRACTION	100
5.8-7.3	0.255	154	0.1993	2733	X-RAY DIFFRACTION	100
7.3-47.71	0.2067	138	0.1744	2901	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	1.9353	0.3463	0.89	0.7678	0.1923	2.3223	0.1097	0.2657	-0.1163	-0.1185	-0.0831	-0.142	-0.0861	0.1949	-0.0098	0.3691	0.0245	-0.017	0.4359	-0.0312	0.3106	-5.6672	20.8523	-5.1416
2	3.8854	-0.7622	-1.1597	3.9039	-1.1658	5.7043	0.3492	-0.5518	-0.0975	-0.0341	-0.1883	0.0817	-0.0577	-0.6242	-0.1254	0.3648	-0.0435	-0.0318	0.5066	-0.0608	0.3759	-31.9004	12.7723	-2.6289
3	2.378	0.2415	0.2747	1.0152	0.5534	1.8898	0.0254	-0.1085	-0.0711	0.0649	0.04	0.0735	0.0881	-0.2003	-0.0549	0.3129	-0.0016	-0.0393	0.3549	0.0512	0.3875	-11.4135	20.2622	14.1644
4	1.6071	0.4467	0.3689	2.0966	0.0121	0.9377	-0.0883	0.1112	-0.0031	-0.3257	0.1398	0.2172	-0.184	-0.0487	-0.0515	0.4316	-0.0507	-0.0131	0.3183	0.0255	0.3908	14.1176	49.2325	20.8869
5	6.6512	0.2606	0.7373	7.8695	0.3556	8.4322	0.0904	0.8925	-1.0745	-0.3952	0.2018	-0.9701	-0.3146	1.3328	-0.3394	0.459	-0.0439	0.0158	0.4177	-0.128	0.5841	39.1744	47.9063	29.4979
6	2.249	1.8741	0.3637	2.252	-0.3192	1.3318	0.0307	-0.134	0.1694	0.1099	0.0478	-0.2028	-0.0989	0.1604	-0.0692	0.3472	0.0037	0.0159	0.3226	-0.0262	0.3491	19.8842	38.1736	32.028
7	1.1624	-0.0093	0.2344	1.4966	0.4142	0.9094	0.0002	0.0348	-0.1429	0.0686	-0.0163	-0.0689	-0.0461	0.0534	0.0105	0.3046	-0.0041	-0.0446	0.3147	0.0249	0.3047	14.0468	31.7256	25.1305
8	3.6944	0.5458	-0.9149	3.1908	-0.9466	3.4479	-0.0678	0.2268	-0.1461	-0.031	-0.0229	-0.5471	0.0187	0.2551	0.154	0.3135	-0.0282	-0.0145	0.4323	-0.0145	0.5275	19.7816	22.9484	17.3888
9	4.6069	-0.5698	0.3109	3.4232	-0.9047	3.6213	-0.0777	-0.3092	-0.0908	0.3023	0.0756	0.2806	-0.1689	-0.1796	-0.0693	0.343	-0.0075	0.0518	0.419	0.0975	0.4406	10.6532	-4.1054	62.6055
10	2.4164	-0.7191	-0.1827	1.6443	0.2426	2.0011	-0.0977	-0.4893	-0.2727	0.1907	0.0439	-0.0658	0.1486	0.2409	0.0216	0.421	0.0299	-0.0061	0.4773	0.1182	0.541	18.861	-16.9656	59.1002
11	2.9947	0.1798	2.1895	2.3874	-1.0973	2.7897	0.2155	0.2767	0.1829	0.1033	-0.1697	-0.1962	0.1436	0.1864	-0.02	0.3546	0.0536	0.0879	0.3343	0.0147	0.3757	45.9057	-17.5879	50.8147
12	0.94	-0.7724	0.1082	1.4917	-0.0484	0.2219	-0.0626	0.1579	0.0652	-0.1726	-0.0952	-0.1655	0.0222	0.0496	0.1696	0.405	-0.0135	0.0089	0.4406	0.125	0.3687	24.9561	-3.6607	44.5713
13	2.0582	-0.1897	0.4708	2.6866	0.4253	2.8361	-0.1716	0.0443	0.1976	0.3033	-0.0402	-0.7239	-0.3122	0.2568	0.1804	0.3926	-0.0268	-0.117	0.4994	0.1877	0.6986	29.6923	15.0141	54.4771
14	2.3602	0.1877	-0.0264	2.6557	1.066	4.124	0.0748	-0.5556	-0.0522	0.8027	-0.1886	0.2773	0.2003	-0.2195	0.0936	0.7504	-0.0286	0.0635	0.6102	0.0126	0.4311	8.817	18.6063	71.4399
15	1.0914	-0.2372	0.2299	1.6899	-0.0115	1.4821	0.0188	-0.2393	0.0192	0.2571	0.0755	0.3324	-0.2173	-0.3139	-0.0829	0.4412	0.0173	0.0761	0.4504	0.092	0.4481	-4.4404	28.4028	54.0251
16	3.3343	1.2529	-1.5612	2.9648	-0.3049	2.1703	0.0203	0.3051	-0.0422	-0.0633	0.3102	0.5677	0.4475	-0.2718	-0.3785	0.3076	-0.0069	-0.0564	0.4136	0.104	0.5026	-6.2041	4.1442	48.5008

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 396 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 9 through 157 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 158 through 182 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 183 through 225 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 226 through 357 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 358 through 396 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 8 through 59 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 60 through 123 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 124 through 182 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 183 through 330 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 331 through 395 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 8 through 97 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 98 through 330 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 331 through 395 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 74 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 4 molecules ABCD

-Non-polymers , 5 types, 74 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 4 molecules ABCD

-
Non-polymers , 5 types, 74 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi