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- PDB-5cli: Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase... -

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Open data

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Basic information

Entry

Database: PDB / ID: 5cli

Title

Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) from the acidophilic bacterium Acetobacter aceti, complexed with AIR (5-aminoimidazole ribonucleotide)

Components

N5-carboxyaminoimidazole ribonucleotide mutase

Keywords

ISOMERASE / acidophile / purine biosynthesis / PurE

Function / homology

Function and homology information

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

Biological species

Acetobacter aceti 1023 (bacteria)

Method

X-RAY DIFFRACTION /

FOURIER SYNTHESIS / Resolution: 1.948 Å

Authors

Starks, C.M. / Kappock, T.J.

Funding support

United States, 3items

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 16, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	5cli.cif.gz	143.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5cli.ent.gz	112.8 KB	Display	PDB format
PDBx/mmJSON format	5cli.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5cli_validation.pdf.gz	445.5 KB	Display	wwPDB validaton report
Full document	5cli_full_validation.pdf.gz	446.7 KB	Display
Data in XML	5cli_validation.xml.gz	17.9 KB	Display
Data in CIF	5cli_validation.cif.gz	26.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cl/5cli ftp://data.pdbj.org/pub/pdb/validation_reports/cl/5cli	HTTPS FTP

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Related structure data

Related structure data	4ycbC 4yccC 4ycdC 4ycjC 5clfC 5clgC 5clhC 5cljC 5ctjC 5cvtC 1u11S 2fwj C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1u11-1 2fwi-1 4ycj-1 2fw7-1 4zmb-1 4zjy-1 5ctj-1 2fwj-1 5bos-1 2fw6-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

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Assembly

Deposited unit

A: N5-carboxyaminoimidazole ribonucleotide mutase

B: N5-carboxyaminoimidazole ribonucleotide mutase

hetero molecules

38.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

defined by author&software
152 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.199, 99.199, 164.389
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-461- HOH
2	1	A-483- HOH

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Components

#1: Protein	N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase Mass: 18882.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetobacter aceti 1023 (bacteria) / Gene: purE, AZ09_02690 / Plasmid: pET23a / Details (production host): pJK283 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase
#2: Chemical	ChemComp-AIR / 5-AMINOIMIDAZOLE RIBONUCLEOTIDE Mass: 295.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₄N₃O₇P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H₂O

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Experimental details

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.02 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M lithium sulfate, 0.1M Tris, 30% (w/v) PEG 4000 (soaked at pH 7)

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Data collection

Diffraction	Mean temperature: 111 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 2, 2005
Radiation	Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.948→40 Å / Num. obs: 30063 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / B_iso Wilson estimate: 17.1 Å² / R_sym value: 0.064 / Net I/σ(I): 23.4
Reflection shell	Resolution: 1.95→2.02 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.494 / Mean I/σ(I) obs: 3.6 / % possible all: 97.1

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 1u11

Resolution: 1.948→35.459 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1734	1281	4.26 %	Random selection
R_work	0.1355	-	-	-
obs	0.1369	30063	98.94 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.948→35.459 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2314	0	19	407	2740

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2500
X-RAY DIFFRACTION	f_angle_d	1.177	3444
X-RAY DIFFRACTION	f_dihedral_angle_d	12.26	921
X-RAY DIFFRACTION	f_chiral_restr	0.049	417
X-RAY DIFFRACTION	f_plane_restr	0.006	441

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 (%)
1.9475-2.0255	0.229	157	0.1955	2989	X-RAY DIFFRACTION	95
2.0255-2.1177	0.2246	166	0.1704	3085	X-RAY DIFFRACTION	98
2.1177-2.2293	0.1907	167	0.154	3080	X-RAY DIFFRACTION	98
2.2293-2.3689	0.1814	162	0.139	3173	X-RAY DIFFRACTION	100
2.3689-2.5518	0.1512	164	0.1334	3187	X-RAY DIFFRACTION	100
2.5518-2.8085	0.161	163	0.1264	3193	X-RAY DIFFRACTION	100
2.8085-3.2147	0.1758	153	0.1283	3231	X-RAY DIFFRACTION	100
3.2147-4.0492	0.1509	149	0.117	3258	X-RAY DIFFRACTION	100
4.0492-35.4652	10000000	0	0.1345	3586	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	1.4763	-1.1809	0.5296	0.9453	-0.4559	4.7263	0.1596	-0.23	0.428	0.4217	-0.0998	0.2371	-0.1773	-0.0365	0.0461	0.1551	0.0173	-0.0033	0.1532	-0.0583	0.2348	-6.5204	29.1406	35.7512
2	8.4013	6.5804	-0.2554	8.4245	-0.2962	1.0987	0.1759	-0.5122	0.0378	0.3079	-0.2589	-0.0136	0.1065	-0.0339	0.0761	0.2087	0.0138	-0.0011	0.2183	-0.0138	0.1255	-0.9875	22.9182	40.8996
3	7.8675	4.7125	0.7109	3.9218	0.4278	0.0855	-0.0108	-0.1401	0.1531	0.0939	-0.0062	-0.0416	-0.0012	0.0081	-0.0036	0.187	0.0072	0.0073	0.1728	-0.0355	0.1521	-8.1992	27.4612	35.9246
4	6.9518	4.6271	-1.6303	6.3532	-2.076	0.6822	-0.2082	0.2402	0.8085	-0.0164	0.2556	0.6246	-0.1888	-0.1895	-0.065	0.1685	0.0419	-0.017	0.1542	-0.0084	0.2072	-16.4838	30.2811	28.142
5	2.1293	-0.2408	0.1442	5.1434	-0.4931	2.6769	-0.0185	0.0501	0.3115	-0.15	-0.1076	0.1388	-0.0958	-0.0979	0.1043	0.1273	0.0107	-0.0032	0.1478	-0.0182	0.1624	-7.7458	26.6634	26.9292
6	4.7614	-2.3074	-4.2756	6.8793	-1.9679	6.6731	0.1268	-0.8525	-0.4569	0.7172	-0.2831	-0.5719	0.1764	0.2938	0.32	0.2215	-0.0534	-0.0438	0.2095	0.0545	0.1741	-4.4657	5.8371	34.4024
7	2.416	1.7391	0.4921	2.7738	0.6183	1.3877	-0.0313	0.0239	0.1251	-0.0012	-0.0248	0.0422	-0.0693	0.0035	0.0603	0.1158	0.0231	0.0042	0.1294	-0.0143	0.1336	0.9663	21.8473	26.4886
8	1.4198	-2.7952	0.4776	6.877	-1.8386	0.8322	0.0468	0.1052	0.0323	-0.1208	-0.0371	-0.0118	0.0015	0.1861	-0.0138	0.162	-0.0197	-0.0339	0.1867	-0.0402	0.1861	14.9224	32.133	35.142
9	7.7949	-5.3848	0.1189	3.809	0.5671	5.6906	-0.0367	-0.2681	-0.0913	0.8002	0.1126	-0.3006	0.5176	0.1728	-0.1025	0.3077	-0.0076	-0.0798	0.205	-0.0689	0.2223	24.1125	14.5733	43.0942
10	2.3936	0.0947	0.0361	0.0059	-0.0441	0.9577	0.0918	0.2279	0.0948	-0.5623	-0.0193	-0.1043	-0.1141	0.1487	-0.0167	0.2519	-0.0317	0.0077	0.209	0.0743	0.1403	13.1411	28.0394	11.5055
11	4.009	-3.366	-1.316	7.0907	2.2679	2.6185	0.1096	0.4258	0.0435	-0.5688	-0.1339	0.1745	-0.0625	-0.326	0.0262	0.2815	-0.0305	-0.0105	0.2699	0.0431	0.1468	6.7629	21.9886	6.0129
12	2.1502	-0.0973	0.3643	1.3902	-0.2648	1.4808	0.0311	0.1524	0.141	-0.1303	-0.0593	-0.2027	-0.0626	0.1625	0.0409	0.1866	-0.0278	0.0099	0.1563	0.0232	0.1498	16.1829	24.7169	17.5195
13	5.2816	2.7824	0.3157	3.9069	1.5836	5.3719	0.0586	0.8114	-0.4765	-1.06	-0.0063	0.2758	0.3648	-0.1125	0.0748	0.3036	0.0363	-0.0105	0.2507	-0.0311	0.1905	5.7973	4.7282	12.095
14	1.5241	-0.9646	0.142	4.081	0.0957	1.95	0.0015	0.0817	0.1221	-0.1137	0.0048	0.0389	-0.0909	-0.0262	-0.0064	0.0934	-0.0204	0.0173	0.1374	0.0147	0.1051	4.312	21.7556	20.3793
15	7.3145	3.9495	2.845	3.4881	2.3166	1.5563	-0.2324	0.0767	0.5566	0.0266	0.3098	0.5927	-0.3513	-0.2132	-0.0725	0.3402	0.02	-0.0467	0.2888	0.1263	0.3303	-6.9135	35.1003	12.0708
16	5.0919	5.7577	3.3137	6.7567	4.9691	8.2401	-0.2386	0.4056	0.2635	-0.4326	0.5913	0.6741	0.133	-0.2693	-0.1819	0.3333	-0.0463	-0.0881	0.3819	0.1107	0.2668	-20.5685	19.6314	3.8564

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 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 179 )

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