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- PDB-4zc8: Structure of Acetobacter aceti PurE-S57T -

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Open data

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Basic information

Entry

Database: PDB / ID: 4zc8

Title

Structure of Acetobacter aceti PurE-S57T

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: 1.754 Å

Authors

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

Citation

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

History

Deposition	Apr 15, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 15, 2016	Group: Other
Revision 1.2	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

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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	4zc8.cif.gz	142.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4zc8.ent.gz	113.3 KB	Display	PDB format
PDBx/mmJSON format	4zc8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zc8_validation.pdf.gz	470.3 KB	Display	wwPDB validaton report
Full document	4zc8_full_validation.pdf.gz	472.1 KB	Display
Data in XML	4zc8_validation.xml.gz	16.9 KB	Display
Data in CIF	4zc8_validation.cif.gz	24.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zc/4zc8 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/4zc8	HTTPS FTP

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Related structure data

Related structure data	4z7jC 5borC 5bosC 4ycbS 1u11 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4zk2-1 2fwa-1 5clf-1 4zjy-1 2fw6-1 5clg-1 5clh-1 4ay4-1 4zmb-1 5bor-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

38.5 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
154 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.775, 99.775, 165.021
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

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Components

#1: Protein	N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase Mass: 18896.738 Da / Num. of mol.: 2 / Mutation: S57T 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
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: 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: 2.49 Å³/Da / Density % sol: 50.7 %
Crystal grow	Temperature: 295 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 225 mm CCD / Detector: CCD / Date: Dec 3, 2011
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: 1.75→50 Å / Num. all: 41986 / Num. obs: 41984 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.6 % / R_merge(I) obs: 0.087 / Net I/σ(I): 45.2
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 14.7 % / R_merge(I) obs: 0.866 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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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

Resolution: 1.754→35.613 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1668	1999	4.76 %	Random selection
R_work	0.1427	-	-	-
obs	0.1438	41964	99.9 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.754→35.613 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2303	0	45	262	2610

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2593
X-RAY DIFFRACTION	f_angle_d	0.96	3565
X-RAY DIFFRACTION	f_dihedral_angle_d	12.185	975
X-RAY DIFFRACTION	f_chiral_restr	0.045	422
X-RAY DIFFRACTION	f_plane_restr	0.005	459

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 (%)
1.7538-1.7977	0.2254	139	0.1974	2788	X-RAY DIFFRACTION	99
1.7977-1.8463	0.2086	142	0.1791	2814	X-RAY DIFFRACTION	100
1.8463-1.9006	0.2026	140	0.1533	2816	X-RAY DIFFRACTION	100
1.9006-1.962	0.1779	141	0.1501	2828	X-RAY DIFFRACTION	100
1.962-2.0321	0.1744	141	0.1474	2805	X-RAY DIFFRACTION	100
2.0321-2.1134	0.1846	141	0.1423	2822	X-RAY DIFFRACTION	100
2.1134-2.2096	0.1666	142	0.1391	2848	X-RAY DIFFRACTION	100
2.2096-2.3261	0.1669	142	0.1382	2831	X-RAY DIFFRACTION	100
2.3261-2.4718	0.1592	142	0.1396	2841	X-RAY DIFFRACTION	100
2.4718-2.6626	0.174	143	0.1474	2852	X-RAY DIFFRACTION	100
2.6626-2.9304	0.1863	143	0.1499	2876	X-RAY DIFFRACTION	100
2.9304-3.3542	0.1536	144	0.1387	2878	X-RAY DIFFRACTION	100
3.3542-4.2248	0.1513	147	0.1271	2913	X-RAY DIFFRACTION	100
4.2248-35.6207	0.1592	152	0.1448	3053	X-RAY DIFFRACTION	99

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	5.723	2.5808	-0.2102	7.3209	-5.6554	7.4927	0.0925	-0.237	0.5015	0.2857	0.1179	0.6115	-0.0847	-0.0326	-0.1431	0.1878	0.0322	0.0127	0.2161	-0.0575	0.2516	-6.2537	29.0963	35.4523
2	4.3847	5.9379	1.2262	8.6807	0.5622	3.5453	0.1568	-0.4276	-0.0241	0.3937	-0.1534	-0.1094	0.2103	-0.0004	0.0023	0.2642	0.015	-0.003	0.2784	-0.0249	0.2439	-0.4257	23.1904	41.26
3	6.4193	4.8378	4.5839	6.0774	3.6474	4.4036	0.0929	-0.4382	0.2062	0.2036	-0.2063	0.0124	-0.0222	-0.2713	0.1344	0.1667	0.0155	0.0116	0.1565	-0.0417	0.1745	-8.068	27.7118	36.1984
4	8.6763	6.5473	-1.3544	5.2511	-1.0251	2.1133	-0.0113	0.2642	0.808	0.1037	0.0612	0.517	-0.0994	-0.2144	-0.0341	0.2249	0.0435	-0.0195	0.1964	-0.0187	0.3286	-16.5424	30.5719	28.4241
5	3.0522	0.0778	0.496	2.3316	0.9026	2.5193	-0.0431	0.0725	0.2841	-0.18	-0.0948	0.1601	-0.1239	-0.0721	0.1329	0.1682	0.0033	-0.0187	0.1788	-0.0108	0.2374	-7.928	26.9188	26.9818
6	4.6067	-2.4437	-0.1207	2.4819	1.7769	2.4731	0.4599	-0.795	-0.5765	1.1088	-0.1073	-0.6584	0.4591	-0.0693	-0.1713	0.3766	-0.0713	-0.0528	0.306	0.0542	0.2747	-4.4999	5.8374	34.6189
7	2.2488	1.6634	0.1897	3.3426	0.4513	1.481	-0.0306	0.0103	0.1308	0.0251	-0.0207	0.0471	-0.1125	0.0446	0.053	0.1561	0.0133	-0.0043	0.1761	-0.0078	0.1837	0.713	21.8622	26.0367
8	3.6543	-3.9013	4.4554	7.583	-4.8861	5.5437	0.0682	0.216	0.0287	-0.0802	-0.1433	0.1501	-0.1073	0.1582	0.071	0.2144	-0.0343	-0.0136	0.2325	-0.0437	0.2632	15.2746	32.3566	35.1626
9	8.2875	-6.572	7.8873	5.7423	-7.1589	9.2849	-0.0642	-0.2582	-0.0481	1.0602	-0.0938	-0.362	0.4245	-0.2399	0.0699	0.3572	-0.0047	-0.0202	0.2755	-0.0673	0.2314	24.3814	15.6455	42.7562
10	7.4892	-1.4931	-0.4079	1.2852	2.6227	6.5785	-0.0287	0.1607	0.3194	-0.6021	0.2041	-0.0013	-0.0872	0.2039	-0.074	0.2415	-0.0506	-0.0085	0.2431	0.062	0.1829	13.4699	28.0716	11.5286
11	5.0153	-3.5259	-2.6691	8.9973	4.4192	5.6464	0.0909	0.4478	0.0416	-0.4965	-0.1423	0.3025	-0.1116	-0.3899	0.0606	0.2258	-0.0373	-0.0375	0.25	0.0412	0.1397	6.8566	22.2125	6.0081
12	1.8173	-0.46	0.0589	2.0124	-0.4809	1.7105	0.0064	0.0881	0.1832	-0.0463	-0.0761	-0.2011	-0.096	0.2073	0.0704	0.2193	-0.0274	-0.0126	0.1999	0.0185	0.2343	16.6624	24.4736	17.6866
13	2.4375	0.0585	2.0376	2.4375	-3.705	7.5074	0.2631	0.7439	-0.3028	-1.3562	-0.1494	0.551	0.7616	0.2044	-0.0482	0.3772	0.0363	-0.0203	0.3324	-0.0401	0.2965	5.8272	4.6443	12.2678
14	1.5379	-0.526	-0.1285	3.344	0.2949	1.7324	-0.0376	0.031	0.1113	-0.1177	0.0479	-0.0281	-0.1167	0.0115	-0.0079	0.1603	-0.0168	-0.0055	0.1943	0.0019	0.1916	4.3523	21.7885	20.2706
15	7.8905	7.2157	0.3234	6.7052	0.6832	1.3774	-0.1436	0.2387	0.7004	0.0279	0.2117	0.7459	-0.305	-0.2524	0.0077	0.4094	0.0496	-0.0912	0.3062	0.0908	0.4679	-6.8403	35.1354	12.3939
16	8.4585	3.3082	2.5896	9.4098	4.651	2.4528	-0.3126	-0.1047	0.122	-0.5015	0.113	0.8082	-0.3501	-0.0873	0.1183	0.3954	-0.0821	-0.0437	0.4061	0.0838	0.28	-20.7569	20.0303	3.9492

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 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 178 )
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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