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- PDB-4zmb: Structure of Acetobacter aceti PurE-S57V,Y154F -

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Open data

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Basic information

Entry

Database: PDB / ID: 4zmb

Title

Structure of Acetobacter aceti PurE-S57V,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: 1.808 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	May 2, 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	4zmb.cif.gz	142.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4zmb.ent.gz	112 KB	Display	PDB format
PDBx/mmJSON format	4zmb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4zmb_validation.pdf.gz	453.3 KB	Display	wwPDB validaton report
Full document	4zmb_full_validation.pdf.gz	453.3 KB	Display
Data in XML	4zmb_validation.xml.gz	17.7 KB	Display
Data in CIF	4zmb_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/4zmb ftp://data.pdbj.org/pub/pdb/validation_reports/zm/4zmb	HTTPS FTP

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Related structure data

Related structure data	4zjyC 4zk2C 4ycbS 1u11 4ycj 4z7j 4zc8 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ycj-1 2fwi-1 4zjy-1 2fw6-1 2fw9-1 2fw7-1 1u11-1 5cvt-1 5clf-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

38.2 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)	99.528, 99.528, 164.447
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-302- HOH
2	1	A-442- HOH
3	1	A-488- HOH

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Components

#1: Protein	N5-carboxyaminoimidazole ribonucleotide mutase / N5-CAIR mutase / 5-(carboxyamino)imidazole ribonucleotide mutase Mass: 18878.764 Da / Num. of mol.: 2 / Mutation: S57V 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 BL21(DE3) (bacteria) / 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.47 Å³/Da / Density % sol: 50.3 %
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-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 2, 2012
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. obs: 37948 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.8 % / R_sym value: 0.093 / Net I/σ(I): 61.14
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 18.7 % / R_merge(I) obs: 0.442 / Mean I/σ(I) obs: 9.79 / % 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: 1.808→42.574 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1677	1810	4.77 %	Same as 4z7j
R_work	0.1365	-	-	-
obs	0.1379	37934	99.58 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.808→42.574 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2314	0	26	388	2728

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2501
X-RAY DIFFRACTION	f_angle_d	1.021	3440
X-RAY DIFFRACTION	f_dihedral_angle_d	11.957	926
X-RAY DIFFRACTION	f_chiral_restr	0.044	417
X-RAY DIFFRACTION	f_plane_restr	0.004	445

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 (%)
1.8076-1.8564	0.2047	130	0.1641	2573	X-RAY DIFFRACTION	95
1.8564-1.911	0.1841	139	0.144	2761	X-RAY DIFFRACTION	100
1.911-1.9727	0.1588	138	0.1314	2753	X-RAY DIFFRACTION	100
1.9727-2.0432	0.1655	137	0.1303	2759	X-RAY DIFFRACTION	100
2.0432-2.125	0.1665	136	0.1342	2748	X-RAY DIFFRACTION	100
2.125-2.2218	0.1818	139	0.1307	2757	X-RAY DIFFRACTION	100
2.2218-2.3389	0.1707	139	0.1317	2768	X-RAY DIFFRACTION	100
2.3389-2.4854	0.1494	138	0.1331	2774	X-RAY DIFFRACTION	100
2.4854-2.6773	0.1818	140	0.1438	2788	X-RAY DIFFRACTION	100
2.6773-2.9466	0.1863	140	0.1474	2796	X-RAY DIFFRACTION	100
2.9466-3.3729	0.1551	142	0.1367	2821	X-RAY DIFFRACTION	100
3.3729-4.2489	0.1547	141	0.1264	2839	X-RAY DIFFRACTION	100
4.2489-42.5856	0.1676	151	0.139	2987	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	2.7322	-1.5956	-0.8394	1.9071	-1.737	5.3563	0.0516	-0.3193	0.3156	0.2168	-0.0769	-0.0593	-0.2214	0.0349	0.0669	0.0798	0.0202	-0.0194	0.1063	-0.0463	0.1288	-5.8213	30.0651	35.7293
2	8.534	5.8775	0.6067	4.4944	0.2346	2.9471	0.081	-0.5513	0.0083	0.1894	-0.2153	0.0473	0.1846	-0.0595	0.0986	0.1467	0.0155	0.0027	0.1676	-0.0231	0.1105	-0.7812	22.8327	40.9882
3	8.8316	5.0128	1.548	3.9749	0.8254	0.5235	0.1084	-0.163	0.2	0.2223	-0.1001	-0.019	0.0199	-0.0155	-0.0181	0.1274	0.0062	-0.0032	0.113	-0.0346	0.0854	-8.1173	27.4836	36.1
4	5.1897	5.5454	-1.7586	7.7549	-2.4711	0.7931	-0.0341	0.2145	0.4956	-0.1318	0.1164	0.4228	-0.092	-0.054	-0.0824	0.1076	0.0395	-0.0193	0.1063	-0.0221	0.1494	-16.4767	30.5052	28.3314
5	1.9173	-0.2986	0.307	5.4138	0.4693	1.5785	-0.0015	0.0247	0.1812	-0.0421	-0.091	0.0116	-0.0864	-0.0874	0.0834	0.0687	-0.0012	0.0047	0.0916	-0.0162	0.0886	-7.5734	26.8278	27.0653
6	5.6605	0.8197	-3.474	2.422	0.146	2.3184	0.1215	-0.6128	-0.8529	0.7431	-0.1859	-0.4958	0.2915	0.1002	0.2495	0.2289	-0.0485	-0.0503	0.2059	0.0596	0.2132	-4.4901	5.8218	34.3792
7	1.5442	0.9447	0.0317	2.3883	-0.2131	1.025	-0.0161	0.013	0.0422	0.0004	-0.034	0.0156	-0.0412	-0.0072	0.0552	0.0683	0.017	-0.0051	0.0904	-0.0123	0.075	0.5077	21.1586	25.9034
8	5.3661	-4.8521	3.0387	5.1314	-2.6878	1.91	0.1202	0.201	-0.0365	-0.1331	-0.1161	0.0445	0.0269	0.1525	0.0424	0.1182	-0.0243	-0.0209	0.1057	-0.0306	0.1233	15.0543	32.1296	35.1073
9	3.5836	-2.4403	-2.4324	3.309	-0.1066	3.6193	0.1375	-0.4037	-0.1686	0.8151	-0.2124	-0.4103	0.5536	0.2051	0.1672	0.3217	-0.0079	-0.1008	0.2091	-0.0229	0.2006	24.3178	14.4818	43.2515
10	3.3208	0.6711	0.4125	0.205	0.5909	3.7418	0.1154	0.2791	0.2301	-0.4103	-0.015	-0.2485	-0.1293	0.0883	-0.0256	0.1447	-0.0202	0.0062	0.1223	0.0432	0.1015	13.501	27.456	11.2887
11	4.257	-3.183	-1.2557	7.1512	2.5397	2.3206	0.0306	0.4018	0.072	-0.3786	-0.1677	0.1285	-0.1047	-0.1957	0.1371	0.2053	-0.0244	-0.0272	0.1914	0.0304	0.0915	6.7165	22.3289	6.0011
12	1.5787	-0.5035	-0.0147	2.1033	-0.3856	1.0064	0.0151	0.0815	0.1336	-0.11	-0.0478	-0.1322	-0.0543	0.1214	0.0446	0.1295	-0.0194	-0.0066	0.1027	0.0175	0.101	16.4902	24.653	17.5517
13	5.2484	4.0856	-0.2479	3.1902	-0.1532	5.0034	-0.1008	0.6348	-0.3695	-0.8312	0.151	0.5168	0.435	0.0886	0.1372	0.23	0.0321	-0.0314	0.1902	-0.0411	0.1594	5.8173	4.7036	12.009
14	0.7133	-0.1224	0.0837	3.0679	0.6795	0.8454	-0.0181	0.0532	0.0352	-0.1371	-0.0025	0.0863	-0.0549	-0.0015	0.0263	0.0702	-0.0067	-0.0009	0.102	0.0077	0.0793	4.4416	20.9327	20.2941
15	6.3412	5.7312	3.6084	5.4157	3.2637	2.7147	-0.2449	-0.1631	0.575	-0.2901	0.0109	0.6995	-0.2146	-0.3485	0.2441	0.2895	0.022	-0.0942	0.2233	0.0675	0.3394	-6.5898	35.5668	12.256
16	6.2188	0.8858	-3.5635	7.0429	-0.0222	2.5948	-0.2734	-0.0756	-0.1232	-0.6328	-0.1223	0.7363	-0.2142	-0.188	0.3974	0.2704	-0.0422	-0.0868	0.2571	0.0697	0.1808	-20.771	20.2263	4.0508

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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