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

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Open data

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Basic information

Entry

Database: PDB / ID: 5clh

Title

Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) H59N from the acidophilic bacterium Acetobacter aceti, at pH 8

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 /

FOURIER SYNTHESIS / Resolution: 1.75 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	5clh.cif.gz	142.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5clh.ent.gz	111 KB	Display	PDB format
PDBx/mmJSON format	5clh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5clh_validation.pdf.gz	456.6 KB	Display	wwPDB validaton report
Full document	5clh_full_validation.pdf.gz	456.7 KB	Display
Data in XML	5clh_validation.xml.gz	17.8 KB	Display
Data in CIF	5clh_validation.cif.gz	27 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cl/5clh ftp://data.pdbj.org/pub/pdb/validation_reports/cl/5clh	HTTPS FTP

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Related structure data

Related structure data	4ycbSC 4yccC 4ycdC 4ycjC 5clfC 5clgC 5cliC 5cljC 5ctjC 5cvtC 2fw7 C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4zjy-1 5clf-1 4z7j-1 5clg-1 5bor-1 4zc8-1 2fwa-1 2fw6-1 5clj-1 5ctj-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)	99.329, 99.329, 164.071
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	B-203- SO4
2	1	B-450- HOH
3	1	B-467- HOH

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Components

#1: Protein	N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase Mass: 18858.666 Da / Num. of mol.: 2 / Mutation: H59N 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-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / 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.: 401 / 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: 2.46 Å³/Da / Density % sol: 50 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: .2 M lithium sulfate, 0.1 M Tris, 30% (w/v) PEG 4000

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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: Sep 18, 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: 1.75→50 Å / Num. obs: 38755 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / B_iso Wilson estimate: 19.55 Å² / R_sym value: 0.049 / Net I/σ(I): 30.5
Reflection shell	Resolution: 1.75→1.81 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.4 / R_sym value: 0.405 / % possible all: 73.1

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Processing

Software

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

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 4ycb chain A

Resolution: 1.75→35.118 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1617	1937	5 %	Random selection
R_work	0.1394	-	-	-
obs	0.1405	38749	92.9 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55 Å² / k_sol: 0.38 e/Å³

Refinement step

Cycle: LAST / Resolution: 1.75→35.118 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2304	0	13	401	2718

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2467
X-RAY DIFFRACTION	f_angle_d	1.187	3393
X-RAY DIFFRACTION	f_dihedral_angle_d	12.195	913
X-RAY DIFFRACTION	f_chiral_restr	0.045	409
X-RAY DIFFRACTION	f_plane_restr	0.007	439

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 (%)
1.7491-1.7929	0.2636	98	0.2542	1967	X-RAY DIFFRACTION	70
1.7929-1.8414	0.221	133	0.1947	2308	X-RAY DIFFRACTION	84
1.8414-1.8955	0.2183	152	0.161	2711	X-RAY DIFFRACTION	97
1.8955-1.9567	0.1954	146	0.1647	2746	X-RAY DIFFRACTION	98
1.9567-2.0266	0.1772	141	0.1532	2736	X-RAY DIFFRACTION	98
2.0266-2.1078	0.1712	141	0.1386	2746	X-RAY DIFFRACTION	98
2.1078-2.2037	0.1617	149	0.1309	2738	X-RAY DIFFRACTION	97
2.2037-2.3199	0.1452	139	0.134	2712	X-RAY DIFFRACTION	97
2.3199-2.4652	0.161	144	0.132	2742	X-RAY DIFFRACTION	96
2.4652-2.6554	0.1661	154	0.1362	2673	X-RAY DIFFRACTION	96
2.6554-2.9226	0.1671	132	0.1411	2710	X-RAY DIFFRACTION	95
2.9226-3.3452	0.1647	146	0.135	2679	X-RAY DIFFRACTION	94
3.3452-4.2134	0.142	140	0.1242	2652	X-RAY DIFFRACTION	92
4.2134-35.1252	0.1324	122	0.1339	2692	X-RAY DIFFRACTION	88

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	4.9055	1.3343	-1.2064	3.1099	-3.9784	5.1455	0.1089	-0.1684	0.5054	0.2699	-0.0388	0.2231	-0.1968	-0.179	0.0388	0.1706	0.0117	-0.0084	0.1676	-0.0635	0.2	-6.2863	29.0583	35.0574
2	9.0797	7.805	-1.0017	9.9542	-1.877	1.2008	0.139	-0.5811	0.0386	0.3024	-0.2228	0.0412	0.1125	0.1007	0.0568	0.2006	0.0096	0.0087	0.2345	-0.0311	0.1148	-1.1374	22.7659	40.8512
3	7.6028	4.7729	3.4557	3.564	2.4152	2.2093	0.1908	-0.3804	0.146	0.2229	-0.1946	-0.0107	0.1118	-0.1595	0.0169	0.1855	-0.0077	-0.0109	0.1853	-0.0432	0.1832	-8.0569	27.7172	36.1322
4	5.7179	5.3253	-1.302	6.6322	-2.3202	1.3165	-0.0378	0.0728	0.5885	-0.0247	0.0703	0.5145	-0.1491	-0.0905	-0.0398	0.168	0.0419	-0.0174	0.1577	-0.03	0.2175	-16.567	30.4207	28.1732
5	2.2215	0.2328	0.511	2.9853	-0.2316	2.0025	-0.0274	-0.0462	0.2478	-0.0174	-0.0768	0.0639	-0.0934	-0.1001	0.075	0.104	0.0032	-0.0028	0.1161	-0.0244	0.1221	-7.6775	26.7417	26.8618
6	2.5454	3.1213	2.8857	4.9554	4.0383	3.493	0.3232	-0.5695	-0.4218	0.7024	-0.1428	-0.4102	0.3857	-0.1381	0.0655	0.2747	-0.0248	-0.0372	0.2674	0.0441	0.2223	-4.448	5.8849	34.3408
7	1.5219	0.933	0.1576	2.0629	0.1683	1.2143	0.0044	-0.0615	0.0697	0.0176	-0.0595	-0.0071	-0.0381	0.0304	0.0698	0.128	0.0097	-0.0031	0.1388	-0.012	0.1353	1.0399	22.3111	26.3204
8	3.817	-3.061	2.2455	5.036	-2.5904	2.0816	0.0655	0.0728	0.0771	-0.0316	-0.0607	0.0387	-0.0313	0.1078	-0.0011	0.1824	-0.0215	-0.0284	0.192	-0.0528	0.1809	14.9895	32.1292	35.0915
9	9.7982	-5.944	1.4064	3.91	-1.4268	9.2642	-0.0335	-0.3948	-0.1689	0.867	-0.0785	-0.5087	0.5686	0.3168	0.024	0.3201	0.0065	-0.0842	0.2146	-0.0508	0.194	23.9655	14.4584	43.2067
10	6.6066	-0.805	-1.3286	1.6833	3.3985	6.8714	-0.0302	0.2323	0.2591	0.051	-0.0017	0.2178	-0.0931	0.2066	0.1202	0.1341	-0.0354	-0.0294	0.154	0.0409	0.0919	13.6067	27.4413	11.3315
11	2.019	-1.6595	-0.6898	6.3359	1.6727	0.546	0.0465	0.2999	0.0643	-0.2368	-0.0867	0.0996	-0.0778	-0.0957	0.0395	0.2371	-0.0134	-0.0132	0.2473	0.0249	0.1292	6.8868	22.2874	5.9909
12	1.4348	-0.4161	0.0125	1.5665	-0.3529	0.6713	0.0198	0.0801	0.1484	-0.0856	-0.0306	-0.1248	-0.0785	0.1061	0.0245	0.1857	-0.0208	-0.0101	0.1608	0.0103	0.1587	16.4222	24.6962	17.5474
13	2.9388	-1.0872	2.6421	3.4978	-3.6835	4.7415	0.1091	0.3184	-0.1319	-0.7862	-0.0119	0.2394	0.4643	0.0796	0.0468	0.2501	0.0276	-0.0155	0.2331	-0.0175	0.1998	5.8399	4.742	12.1327
14	1.206	-0.9343	0.1119	4.6959	0.0238	1.2465	-0.0212	0.0071	0.0947	-0.0344	0.0141	0.0474	-0.0572	-0.0108	0.0153	0.0871	-0.0176	0.014	0.128	0.005	0.0976	4.6416	21.6494	20.5091
15	6.5832	5.682	1.0023	7.0776	1.655	0.9703	-0.1231	0.1382	0.5191	-0.1133	0.1165	0.2102	-0.196	-0.1485	0.0286	0.2636	0.0138	-0.0476	0.2227	0.0859	0.2825	-6.6696	35.3171	12.1343
16	5.2676	5.5148	-2.7803	5.9312	-3.7274	7.7863	-0.4603	0.5245	0.1737	-0.2044	0.6166	0.659	0.0762	-0.3371	-0.1498	0.2144	-0.0164	-0.0625	0.2638	0.059	0.2287	-20.6768	20.0789	4.2578

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 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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