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- PDB-4zk2: Structure of Acetobacter aceti PurE-S57D -

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Open data

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Basic information

Entry

Database: PDB / ID: 4zk2

Title

Structure of Acetobacter aceti PurE-S57D

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: 2.749 Å

Authors

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

Citation

Journal: To be published
Title: Serine mutants of Acetobacter aceti PurE
Authors: Sullivan, K.L. / Kappock, T.J.

History

Deposition	Apr 29, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 11, 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

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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	4zk2.cif.gz	131.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4zk2.ent.gz	103.3 KB	Display	PDB format
PDBx/mmJSON format	4zk2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zk2_validation.pdf.gz	443.3 KB	Display	wwPDB validaton report
Full document	4zk2_full_validation.pdf.gz	443.9 KB	Display
Data in XML	4zk2_validation.xml.gz	13.1 KB	Display
Data in CIF	4zk2_validation.cif.gz	17.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zk/4zk2 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/4zk2	HTTPS FTP

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Related structure data

Related structure data	4zjyC 4zmbC 4ycbS 1u11 4z7j 4zc8 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2fw6-1 4zc8-1 2fw1-1 5bor-1 4ycc-1 5ctj-1 2fw8-1 2fwa-1 5clf-1 4zmb-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

37.9 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)	99.703, 99.703, 165.606
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: 18910.721 Da / Num. of mol.: 2 / Mutation: S57D 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A063X4U8, 5-(carboxyamino)imidazole ribonucleotide mutase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.5 Å³/Da / Density % sol: 50.8 %
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 300 mm CCD / Detector: CCD / Date: Nov 24, 2013
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: 2.749→50 Å / Num. all: 11217 / Num. obs: 11198 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / R_merge(I) obs: 0.117 / Net I/σ(I): 23.3
Reflection shell	Resolution: 2.749→2.8 Å / Redundancy: 10.9 % / R_merge(I) obs: 0.738 / % possible all: 99.4

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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: 2.749→49.852 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2205	534	4.77 %	Same as 4ZC8
R_work	0.1725	-	-	-
obs	0.1747	11184	99.42 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.749→49.852 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2305	0	8	38	2351

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2393
X-RAY DIFFRACTION	f_angle_d	1.123	3275
X-RAY DIFFRACTION	f_dihedral_angle_d	11.609	861
X-RAY DIFFRACTION	f_chiral_restr	0.045	395
X-RAY DIFFRACTION	f_plane_restr	0.006	421

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 (%)
2.7495-3.0261	0.2541	132	0.2332	2605	X-RAY DIFFRACTION	99
3.0261-3.4639	0.2361	130	0.198	2617	X-RAY DIFFRACTION	100
3.4639-4.3638	0.2141	134	0.1578	2651	X-RAY DIFFRACTION	100
4.3638-49.8597	0.2091	138	0.156	2777	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	7.5455	4.9563	-1.8693	3.8481	-2.7291	5.2183	-0.1097	-0.2196	1.012	0.0155	0.7122	1.6391	0.2946	-0.2095	-0.2562	0.4241	0.0518	-0.0147	0.4302	-0.0681	0.4744	-6.3368	29.2082	35.4144
2	7.8843	5.4334	4.174	3.8461	2.9892	6.4115	0.1461	-0.4814	-0.1865	0.437	0.0474	0.1766	0.2661	0.1776	-0.1174	0.3791	0.0229	0.031	0.5029	-0.0398	0.3512	-0.934	23.0674	41.2122
3	5.9204	6.1405	5.5243	7.5439	4.9337	7.1764	0.3812	-0.403	0.4832	0.5249	-0.3932	0.1553	0.2018	-0.0823	-0.0049	0.3808	0.0765	-0.0217	0.41	-0.0405	0.3669	-8.372	27.5157	36.2228
4	8.4251	7.4839	-2.8852	8.5662	-2.9522	4.0112	0.8849	0.4071	0.7758	0.6248	-0.2582	1.0849	-1.0113	-0.585	-0.4418	0.5771	0.1581	0.0148	0.4509	-0.1271	0.6086	-16.5138	30.1423	28.7578
5	3.8974	1.2305	0.9566	1.4042	1.0757	6.501	-0.0258	0.136	0.2493	-0.2033	-0.1399	0.1283	-0.0565	0.1445	0.1414	0.3505	0.0038	0.0299	0.3587	-0.0222	0.3401	-7.5309	26.7029	27.0055
6	1.283	-1.7505	-1.8196	4.5957	4.4503	4.3342	0.9842	-1.2222	-0.4681	2.4296	-0.0221	-0.2745	0.9829	-0.0236	-0.529	0.6081	-0.1573	0.0376	0.7733	0.0305	0.4503	-4.4974	5.8708	34.5999
7	4.026	2.5452	0.2262	8.1126	1.2254	3.8808	0.0451	-0.0083	0.1021	0.3507	-0.0034	-0.0378	-0.1102	0.3062	-0.055	0.2684	0.0319	0.0008	0.2963	-0.0166	0.2565	1.0885	22.5728	26.5684
8	4.794	-4.7082	5.9346	4.6269	-5.8264	7.3401	0.1726	-0.0481	0.5628	0.1239	-0.268	-0.2071	-0.4375	0.4101	0.1226	0.4478	-0.0604	0.0304	0.3722	-0.042	0.4127	14.9809	32.3997	35.3811
9	6.0969	1.7129	1.2067	8.1306	-3.6627	9.1687	0.6413	0.6356	0.1354	1.2631	-0.8556	-0.6522	-0.0373	-0.2288	-0.5594	0.4482	0.1087	-0.0338	0.4529	-0.0945	0.3724	24.3179	15.0516	42.8386
10	5.7073	-0.9821	-1.7232	7.5933	7.7264	7.9573	-0.3165	0.2873	0.0165	-0.2562	0.0001	0.7412	0.1289	0.0175	0.2091	0.3609	-0.0536	-0.056	0.5102	0.1311	0.3002	13.3628	28.3322	11.6231
11	6.0802	-2.2816	-0.6339	3.4016	1.6777	8.247	0.052	0.3495	0.0078	-0.9518	0.3671	-0.1034	0.1229	-0.7563	-0.4576	0.5124	-0.0684	-0.0578	0.5234	0.0477	0.3417	6.6998	22.6314	6.0558
12	4.2554	-2.7232	0.2559	6.3494	-0.5155	1.7444	0.1121	0.0859	0.3039	-0.143	-0.1248	-0.3888	-0.1045	0.2675	0.026	0.4728	-0.0628	-0.0028	0.4343	0.0333	0.3109	16.1982	24.5998	17.5795
13	5.2797	-4.2039	0.7076	7.398	-1.0187	8.419	0.671	2.5208	-0.7243	-3.1216	-0.486	0.3384	0.2582	0.2402	-0.0397	0.6682	0.0082	0.0168	0.7179	0.0025	0.448	5.8945	4.8117	12.2751
14	3.579	-1.5937	-0.4681	5.786	-0.3143	1.5235	-0.0677	-0.08	0.0903	-0.1882	0.0824	-0.2156	-0.1627	-0.0551	0.0023	0.3357	-0.0171	-0.0216	0.3391	-0.0122	0.2543	4.4004	21.9942	20.5003
15	2.6227	2.7372	2.9375	2.8622	3.082	3.7938	-0.2131	-0.0352	1.173	-0.5582	-0.0065	0.6516	-0.2574	-0.7255	0.2143	0.53	0.0674	-0.1182	0.3994	0.0944	0.554	-6.8374	35.4059	12.1452
16	9.5076	5.4268	4.9209	5.955	5.8278	5.7366	0.1386	0.521	0.3762	-0.4767	-0.6285	0.9234	0.422	-0.6126	0.2518	0.572	-0.074	-0.1209	0.6981	-0.0071	0.4934	-20.7555	19.8939	3.9116

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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