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- PDB-5bor: Structure of Acetobacter aceti PurE-S57C, sulfonate form -

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Open data

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Basic information

Entry

Database: PDB / ID: 5bor

Title

Structure of Acetobacter aceti PurE-S57C, sulfonate form

Components

N5-carboxyaminoimidazole ribonucleotide mutase

Keywords

ISOMERASE / acidophile / PurE / purine biosynthesis

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 /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2 Å

Authors

Sullivan, K.L. / Kappock, T.J.

Citation

Journal: To Be Published
Title: Mutation of the conserved serine in two PurE classes
Authors: Sullivan, K.L. / Kappock, T.J.

History

Deposition	May 27, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 15, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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	5bor.cif.gz	141.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5bor.ent.gz	111.2 KB	Display	PDB format
PDBx/mmJSON format	5bor.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/bo/5bor ftp://data.pdbj.org/pub/pdb/validation_reports/bo/5bor	HTTPS FTP

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Related structure data

Related structure data	4z7jC 4zc8C 5bosC 4ycbS 1u11 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ycd-1 2fw1-1 4ycj-1 5bos-1 4zjy-1 5clf-1 2fwb-1 2fw6-1 5ctj-1 5clh-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

38.3 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
153 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.527, 99.527, 165.792
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-304- HOH
2	1	A-434- HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein

N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase

Mass: 18946.773 Da / Num. of mol.: 2 / Mutation: S57C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acetobacter aceti 1023 (bacteria) / Gene: purE, AZ09_02690 / Plasmid: pET23a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase

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Non-polymers , 5 types, 268 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.48 Å³/Da / Density % sol: 50.4 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 25% (v/v) PEG 4000, 0.1 M Tris-HCl, 0.2 M lithium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 27, 2012
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.9996→50 Å / Num. obs: 28501 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.7 % / B_iso Wilson estimate: 27.3 Å² / R_sym value: 0.122 / Net I/σ(I): 34.04
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 12.4 % / R_merge(I) obs: 0.802 / Mean I/σ(I) obs: 3.875 / % possible all: 99.9

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4ycb chain A

Resolution: 2→35.714 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1755	1362	4.78 %	Same as 4z7j
R_work	0.1396	-	-	-
obs	0.1412	28495	99.83 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→35.714 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2320	0	22	262	2604

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2504
X-RAY DIFFRACTION	f_angle_d	0.985	3443
X-RAY DIFFRACTION	f_dihedral_angle_d	12.162	923
X-RAY DIFFRACTION	f_chiral_restr	0.043	412
X-RAY DIFFRACTION	f_plane_restr	0.005	443

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 (%)
1.9996-2.0711	0.2283	132	0.1759	2643	X-RAY DIFFRACTION	99
2.0711-2.154	0.2223	139	0.162	2647	X-RAY DIFFRACTION	100
2.154-2.252	0.2103	129	0.1513	2697	X-RAY DIFFRACTION	100
2.252-2.3707	0.2142	138	0.1485	2694	X-RAY DIFFRACTION	100
2.3707-2.5192	0.1638	133	0.1448	2666	X-RAY DIFFRACTION	100
2.5192-2.7137	0.1972	132	0.145	2697	X-RAY DIFFRACTION	100
2.7137-2.9866	0.195	140	0.1481	2698	X-RAY DIFFRACTION	100
2.9866-3.4185	0.1699	136	0.1385	2742	X-RAY DIFFRACTION	100
3.4185-4.3058	0.1459	136	0.1228	2753	X-RAY DIFFRACTION	100
4.3058-35.72	0.1571	147	0.133	2896	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	6.133	-0.4769	-0.7275	4.4906	-3.6666	3.4079	0.2192	-0.3243	0.5209	0.4553	-0.1438	-0.012	-0.1231	-0.0387	0.0503	0.2574	-0.0117	-0.0041	0.2566	-0.0609	0.2253	-5.917	30.2905	35.8937
2	5.1367	4.8701	-0.6943	4.8504	-1.0049	3.5013	0.1402	-0.5144	0.0707	0.1935	-0.1644	0.0216	0.1176	-0.0356	0.0376	0.2786	0.0357	0.0019	0.3009	-0.0242	0.2321	-0.8632	23.0123	41.3377
3	7.9915	6.102	5.3476	7.0055	4.3791	4.556	0.1711	-0.2742	0.0603	0.2013	-0.1771	-0.07	0.0464	-0.1977	0.0273	0.1988	0.0097	0.0076	0.1806	-0.042	0.182	-8.3712	27.2502	36.2138
4	9.5599	7.3948	-4.1138	6.1853	-3.3844	1.8606	-0.001	0.4404	0.7188	0.1153	0.1793	0.6151	-0.254	-0.1563	-0.1777	0.2215	0.0626	-0.0248	0.1994	-0.02	0.2869	-16.5965	30.4644	28.5883
5	2.639	0.9768	0.1591	3.9253	1.148	2.2387	0.0056	0.0469	0.2171	-0.1187	-0.1349	0.1321	-0.0914	-0.0776	0.1148	0.1483	0.0075	-0.0136	0.1803	-0.011	0.1723	-7.6779	26.825	27.2724
6	5.5965	-3.2411	-1.7167	5.4695	-0.5934	1.2285	0.2367	-1.1953	-0.7913	1.6767	-0.0953	-0.3856	0.6253	0.034	0.0713	0.4668	-0.089	-0.0512	0.4384	0.0941	0.2833	-4.63	5.8659	34.8528
7	2.5352	2.1894	0.3716	4.243	0.5242	1.6956	-0.0266	0.0591	0.1211	0.0544	-0.0248	0.0528	-0.0704	0.0315	0.059	0.1448	0.0243	-0.0047	0.1866	-0.008	0.1691	0.7118	22.2474	26.1959
8	8.6447	-7.8394	7.9914	7.8245	-7.2508	8.545	0.0758	0.2036	-0.0424	0.0364	-0.1435	0.0091	-0.2616	0.3032	0.121	0.1781	-0.0479	0.0015	0.2054	-0.0452	0.2075	15.063	32.1957	35.4661
9	5.1272	-5.0384	2.3115	5.0331	-1.4929	8.4269	-0.1945	-0.5802	-0.1159	1.1075	0.5143	-0.3113	0.8208	0.0268	-0.277	0.4523	0.0223	-0.0748	0.3316	-0.0496	0.3272	24.1546	14.4588	43.6321
10	7.4102	-0.6661	-2.1763	2.7596	4.4827	8.1593	-0.0682	0.2002	0.3302	-0.1308	0.0009	-0.0946	-0.0165	0.3069	0.0943	0.2006	-0.0407	-0.0465	0.2504	0.0626	0.1841	13.3231	28.1196	11.7094
11	4.8843	-3.8856	-0.5356	7.5708	1.1267	3.5802	0.1113	0.3993	0.0304	-0.4372	-0.064	0.161	-0.0609	-0.3312	-0.0357	0.3074	-0.0261	-0.0381	0.2968	0.0282	0.1779	6.6108	22.4743	6.1824
12	2.1334	-0.7064	0.1388	2.298	-0.4207	1.5135	0.0444	0.0737	0.1431	-0.13	-0.0587	-0.1911	-0.0555	0.1784	0.0309	0.2553	-0.0378	-0.0088	0.2166	0.0235	0.2187	16.4055	24.5993	17.7387
13	1.6232	1.1312	-2.1252	0.7995	-1.2759	6.6213	0.2739	1.2582	-0.6963	-1.792	-0.1705	0.848	0.5519	-0.3151	0.0049	0.494	0.0555	-0.0826	0.4385	-0.0686	0.3701	5.8603	4.6762	12.4237
14	1.4774	-1.2336	-0.0363	5.9917	0.7496	1.837	-0.0222	0.0261	0.0856	-0.1345	0.0285	0.0108	-0.0682	0.0003	0.0135	0.1183	-0.0226	0.0068	0.1968	0.0177	0.1417	4.4454	21.8575	20.659
15	4.6211	5.3437	3.0489	6.2884	3.22	3.0905	-0.2838	0.0353	0.7224	-0.3586	0.2055	0.6696	-0.3445	-0.3845	0.143	0.3664	0.0373	-0.0607	0.309	0.087	0.3955	-6.9456	35.2481	12.0938
16	3.825	5.4057	-2.8188	8.885	-1.0908	9.713	-0.1901	0.1265	0.1594	-0.6575	0.0507	0.9421	0.2063	-0.0447	0.229	0.3392	0.0116	-0.0859	0.3552	0.0525	0.3536	-20.5352	19.8474	4.0113

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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