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- PDB-4ycj: Structure of Acetobacter aceti PurE Y154F -

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Open data

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Basic information

Entry

Database: PDB / ID: 4ycj

Title

Structure of Acetobacter aceti PurE Y154F

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: 1.845 Å

Authors

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

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	Feb 20, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 24, 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 / diffrn_radiation_wavelength / 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	4ycj.cif.gz	141.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ycj.ent.gz	111.4 KB	Display	PDB format
PDBx/mmJSON format	4ycj.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/yc/4ycj ftp://data.pdbj.org/pub/pdb/validation_reports/yc/4ycj	HTTPS FTP

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Related structure data

Related structure data	4ycbSC 4yccC 4ycdC 5clfC 5clgC 5clhC 5cliC 5cljC 5ctjC 5cvtC 1u11 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5clf-1 4zjy-1 2fwi-1 1u11-1 4zmb-1 5ctj-1 2fw7-1 4ycd-1 2fw6-1 5cvt-1 2fw1-1 2fwb-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 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)	99.761, 99.761, 165.008
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: 18866.711 Da / Num. of mol.: 2 / Mutation: Y154F 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 355 / 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: 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: 0.9785 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: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 1.842→50 Å / Num. obs: 36064 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12 % / R_sym value: 0.09 / Net I/σ(I): 44.1
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 5.36 / R_sym value: 0.421 / % 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 CHAIN A

Resolution: 1.845→32.598 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1895	1510	4.19 %	same as 4YCB
R_work	0.1774	-	-	-
obs	0.178	36064	99.8 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.845→32.598 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2329	0	13	355	2697

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2489
X-RAY DIFFRACTION	f_angle_d	1.171	3424
X-RAY DIFFRACTION	f_dihedral_angle_d	11.749	926
X-RAY DIFFRACTION	f_chiral_restr	0.051	415
X-RAY DIFFRACTION	f_plane_restr	0.006	444

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 (%)
1.8454-1.9049	0.4356	2	0.2198	3198	X-RAY DIFFRACTION	98
1.9049-1.973	0.3157	29	0.2165	3189	X-RAY DIFFRACTION	100
1.973-2.052	0.2235	179	0.2077	3062	X-RAY DIFFRACTION	100
2.052-2.1454	0.2361	158	0.2052	3082	X-RAY DIFFRACTION	100
2.1454-2.2585	0.2161	182	0.1885	3059	X-RAY DIFFRACTION	100
2.2585-2.3999	0.2439	154	0.19	3100	X-RAY DIFFRACTION	100
2.3999-2.5852	0.184	155	0.1874	3119	X-RAY DIFFRACTION	100
2.5852-2.8452	0.2158	168	0.1887	3108	X-RAY DIFFRACTION	100
2.8452-3.2566	0.186	169	0.1734	3123	X-RAY DIFFRACTION	100
3.2566-4.1016	0.1738	160	0.1568	3180	X-RAY DIFFRACTION	100
4.1016-32.6034	0.1459	154	0.153	3334	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	3.5216	-0.4077	0.7933	3.2202	2.9859	3.1649	0.1596	-0.2756	-0.3854	0.5551	-0.1117	-0.0086	0.1829	-0.1422	0.0208	0.1882	-0.011	0.0071	0.1729	0.0594	0.194	105.704	69.3959	35.6291
2	5.6213	3.6533	-0.1202	5.3543	-0.2266	1.5012	-0.0021	-0.5087	0.011	0.1836	-0.0879	0.0759	-0.0747	-0.069	0.0718	0.1974	0.0045	0.0128	0.2222	0.0247	0.1326	100.8803	76.9671	41.0336
3	4.7659	1.6275	-0.9369	1.2729	-0.624	0.9908	0.0133	-0.4041	-0.1828	0.1431	-0.0537	0.0407	0.0047	0.0666	0.0549	0.1764	0.0098	0.013	0.1627	0.0373	0.1527	107.8885	72.0309	36.1655
4	3.0871	2.1502	0.7879	3.6056	0.615	0.8397	-0.0026	0.0923	-0.4133	0.1739	-0.0198	-0.2243	0.0258	0.1125	-0.0152	0.1717	0.034	0.0064	0.1819	0.031	0.2326	116.3398	69.0115	28.2783
5	2.041	0.0151	-0.2372	1.4031	-0.8066	1.6022	-0.043	0.0122	-0.2222	-0.0574	-0.0243	-0.0766	0.0969	0.0008	0.0732	0.1298	-0.0007	0.0064	0.1204	0.0167	0.146	107.2956	72.7576	27.0841
6	1.6312	0.593	0.4509	2.0634	-2.3103	3.5438	0.2193	-0.8737	0.5415	0.9491	-0.2318	0.2548	-0.4832	-0.0171	0.2798	0.3201	-0.0618	0.0314	0.297	-0.0653	0.2521	104.3331	93.957	34.5315
7	1.3539	0.6287	-0.0106	1.5573	0.1618	0.7434	-0.0273	-0.0055	-0.0301	0.0523	-0.0039	-0.0031	0.0836	-0.0397	0.0551	0.1416	-0.0027	0.0119	0.1451	0.0074	0.1344	98.814	78.4109	26.5318
8	2.3755	-2.7879	-1.0325	5.4847	1.5205	0.944	0.1096	-0.0044	-0.0475	-0.0916	-0.0686	-0.0315	-0.0582	-0.1146	-0.0389	0.1955	-0.0427	0.0311	0.2074	0.0436	0.1904	84.6602	67.5002	35.2078
9	9.8467	-4.047	-0.0697	8.4365	-0.466	4.0375	0.1343	-0.3656	0.3778	0.8301	-0.1613	0.3902	-0.6092	-0.2147	-0.0223	0.3277	0.0011	0.1081	0.2338	0.0357	0.1827	75.5372	85.2589	43.3856
10	4.1153	-1.3437	0.3556	5.3797	-2.9836	2.4526	0.0558	0.27	-0.2089	-0.3543	-0.0243	0.1015	0.0775	-0.0691	-0.037	0.202	-0.0166	0.0088	0.2013	-0.044	0.1494	85.9678	72.1848	11.3621
11	1.9704	-0.9293	0.2617	3.4501	-0.581	1.1754	0.0272	0.2831	0.021	-0.1596	-0.0428	-0.1904	0.0042	0.1916	0.0446	0.2303	-0.0117	0.0186	0.2622	-0.0043	0.1654	92.7571	77.344	6.0179
12	1.7266	-0.3268	0.0822	1.1413	0.169	1.0512	0.0128	0.0281	-0.142	-0.027	-0.0426	0.1694	0.053	-0.1486	0.0454	0.1568	-0.0264	0.0177	0.151	-0.0108	0.1642	83.2107	75.0435	17.5436
13	8.3672	2.4258	-3.3636	4.6403	2.6131	4.6679	0.1523	0.7532	0.4606	-0.823	-0.2031	-0.2402	-0.5419	-0.2502	-0.0598	0.2705	0.036	0.0319	0.2451	0.0373	0.2334	93.6823	94.9389	12.345
14	0.9542	-0.4207	0.0364	2.1013	-0.3442	0.6674	-0.0526	0.0329	-0.009	-0.0236	-0	-0.088	0.0302	-0.001	0.0366	0.1443	-0.0118	0.0113	0.1655	-0.0041	0.1508	95.2523	78.7836	20.3874
15	6.1619	4.4212	-1.4894	4.2356	-1.1119	0.457	-0.1974	0.0316	-0.3966	-0.1596	0.1248	-0.3491	0.1727	0.0976	0.0637	0.2646	0.0144	0.0482	0.2175	-0.0499	0.2189	105.8989	63.9746	12.4992
16	9.2738	2.2948	-0.4561	4.8964	0.3027	6.459	-0.1445	0.4888	0.3996	-0.6498	0.1323	-0.4486	-0.3867	0.2412	0.0481	0.3335	-0.0174	0.054	0.3167	-0.0332	0.2187	121.1676	81.7985	2.1353

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 181 )

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