PDB-4ehi: An X-ray Crystal Structure of a putative Bifunctional Phosphoribo...

ID or keywords:

Entry

Database: PDB / ID: 4ehi

Title

An X-ray Crystal Structure of a putative Bifunctional Phosphoribosylaminoimidazolecarboxamide Formyltransferase/IMP Cyclohydrolase

Components

Bifunctional purine biosynthesis protein PurH

Keywords

HYDROLASE /

TRANSFERASE /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

phosphoribosylaminoimidazolecarboxamide formyltransferase /

phosphoribosylaminoimidazolecarboxamide formyltransferase activity /

IMP cyclohydrolase /

IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process
Similarity search - Function

Biological species

Campylobacter jejuni subsp. jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.28 Å

Authors

Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Kwok, J. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: An X-ray Crystal Structure of a putative Bifunctional Phosphoribosylaminoimidazolecarboxamide Formyltransferase/IMP Cyclohydrolase
Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Kwok, J. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases

History

Deposition	Apr 2, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 6, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ehi.cif.gz	407.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ehi.ent.gz	347.7 KB	Display	PDB format
PDBx/mmJSON format	4ehi.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/eh/4ehi ftp://data.pdbj.org/pub/pdb/validation_reports/eh/4ehi	HTTPS FTP

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Related structure data

Similar structure data	3igh-1 1zcz-d 3cnt-d 4rpb-d 3bi4-d 5zic-d 1tzm-d 4upa-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
Other databases	TargetTrack: IDP90570

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (5)

Deposited unit

A: Bifunctional purine biosynthesis protein PurH

B: Bifunctional purine biosynthesis protein PurH

hetero molecules

121 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

A: Bifunctional purine biosynthesis protein PurH

hetero molecules

B: Bifunctional purine biosynthesis protein PurH

hetero molecules

defined by software
121 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	93.881, 101.234, 114.294
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Bifunctional purine biosynthesis protein PurH / Phosphoribosylaminoimidazolecarboxamide formyltransferase / AICAR transformylase / IMP ...Phosphoribosylaminoimidazolecarboxamide formyltransferase / AICAR transformylase / IMP cyclohydrolase / ATIC / IMP synthase / Inosinicase Mass: 59875.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: NCTC 11168 / Gene: Cj0953c, purH / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplus(de3) Ril References: UniProt: Q9PNY2, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase
#2: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.27 Å³/Da / Density % sol: 45.76 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20%PEG 3350, 0.2M Na Sulfate, 0.1M Bis-Tris, 5.8mg/mL protein, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2010 / Details: Be Lenes
Radiation	Monochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.28→29.48 Å / Num. all: 48301 / Num. obs: 48301 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / B_iso Wilson estimate: 42.72 Å² / R_merge(I) obs: 0.095 / Net I/σ(I): 36.75
Reflection shell	Resolution: 2.28→2.3 Å / Redundancy: 10.4 % / R_merge(I) obs: 0.549 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
BLU-MAX		data collection
PHENIX		model building
BUSTER	2.10.0	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.28→29.48 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.923 / SU R Cruickshank DPI: 0.297 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	1989	4.12 %	RANDOM
R_work	0.173	-	-	-
obs	0.174	48301	96 %	-
all	-	48301	-	-

Displacement parameters

B_iso mean: 47.17 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.5136 Å²	0 Å²	0 Å²
2-	-	-2.8514 Å²	0 Å²
3-	-	-	-4.6621 Å²

Refine analyze

Luzzati coordinate error obs: 0.26 Å

Refinement step

Cycle: LAST / Resolution: 2.28→29.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7678	0	59	554	8291

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	7901	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.06	10638	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		3730	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		229	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		1131	HARMONIC	5
X-RAY DIFFRACTION	t_it		7901	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.19
X-RAY DIFFRACTION	t_other_torsion	2.85
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		1026	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		9305	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.28→2.34 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2154	103	4.37 %
R_work	0.1886	2254	-
all	0.1898	2357	-
obs	-	-	96 %

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	2.8881	-0.7361	-0.6772	3.2676	-0.1585	2.5746	0.083	0.5038	-0.0595	-0.1978	-0.0956	-0.0092	0.0091	0.1474	0.0126	-0.0695	0.0528	-0.0184	0.021	-0.022	-0.0887	46.394	20.3892	-26.0072
2	1.8557	-1.9109	0.8608	3.3735	-1.6722	4.0368	0.0368	0.424	-0.0199	-0.17	-0.0341	0.1554	-0.0371	-0.0436	-0.0027	-0.052	0.0616	0.0022	0.0577	-0.0749	-0.0397	43.6882	16.7507	-27.351
3	3.1907	-1.331	-1.1408	1.1649	0.2737	1.1442	-0.0139	0.3593	0.0514	0.0303	-0.0043	0.0087	-0.1042	-0.1195	0.0182	0.0069	0.0344	-0.0026	-0.0067	-0.0135	-0.028	35.9597	24.2291	-13.3266
4	2.3173	-0.2683	-1.1299	0.6384	0.2067	1.4174	0.0173	-0.0798	0.0781	0.0111	-0.0232	-0.0785	-0.031	0.105	0.0059	0.0007	0.0067	-0.0149	-0.0705	-0.0349	-0.0392	41.5091	26.9197	-7.2467
5	1.3379	-0.1448	-1.0897	1.5273	0.895	0.7647	0.176	0.0004	-0.0042	-0.102	-0.0148	-0.2564	0.0143	0.1734	-0.1612	-0.0454	-0.0068	0.0271	-0.001	-0.0211	-0.068	45.6569	43.2953	5.2815
6	3.3671	-0.9091	-0.7289	2.7471	0.351	2.2274	0.1737	-0.0967	0.4836	-0.1029	-0.047	-0.1912	-0.2855	0.3258	-0.1267	-0.0405	-0.0305	0.0618	-0.0757	-0.0324	-0.0515	41.1152	62.9573	9.4899
7	0.5419	-0.357	0.4012	1.6186	0.312	1.6314	0.0635	0.1911	0.0985	-0.2799	-0.0401	0.0567	-0.046	0.129	-0.0235	-0.0464	0.0601	0.0466	0.0145	0.0093	-0.0473	39.0943	50.6316	4.6933
8	0	-0.8951	-0.633	2.3161	1.1275	0.9089	0.1168	-0.0268	0.0429	-0.1234	-0.2853	0.0056	-0.1098	-0.2116	0.1685	-0.0388	0.0277	-0.0163	-0.0119	-0.0601	0.0055	19.6347	48.6766	15.0592
9	1.2644	1.3824	3.0305	1.9213	-0.8994	3.0621	-0.0061	0.1675	0.0618	-0.1095	0.0282	0.059	-0.0229	-0.0791	-0.0221	0.1139	0.0897	0.0569	0.0608	-0.0163	0.0074	17.8134	67.3044	15.1258
10	4.7642	0.4821	-1.4916	5.1056	1.1363	3.1541	0.0535	-0.3983	0.0057	0.2891	0.0048	-0.3511	-0.0663	-0.0646	-0.0583	-0.0717	0.0012	0.0328	-0.0817	-0.0651	-0.0513	30.318	59.8708	25.0511
11	3.4312	-1.0198	-1.3706	1.9865	0.3653	2.8624	-0.0532	-0.1982	-0.0888	0.121	-0.0377	-0.1621	0.0625	-0.1101	0.0909	-0.0041	0.0438	0.0476	-0.062	-0.0937	-0.0498	19.698	59.7571	29.1295
12	0.1959	-1.6341	-0.7429	3.5947	2.1977	1.7614	-0.023	-0.0464	-0.0962	0.2513	-0.1456	0.0821	0.0307	-0.2597	0.1686	-0.0522	0.0506	0.0411	0.0236	-0.0792	0.0012	14.6582	56.8048	27.1511
13	2.4023	0.1976	0.9232	1.7033	0.3293	2.347	0.2082	-0.1945	-0.5659	0.1103	-0.0202	-0.0666	0.4703	-0.1238	-0.188	-0.0691	-0.0029	-0.0416	-0.0689	-0.0174	-0.0155	25.0729	-1.7313	-3.392
14	2.7685	3.2209	-1.4026	1.8615	-0.8417	0	-0.0192	0.2642	-0.024	-0.1615	0.0232	-0.1593	0.1857	0.0995	-0.0041	-0.0323	0.0295	-0.0029	0.0632	-0.1178	-0.0441	26.3028	4.1595	-15.0095
15	3.6723	0.4591	1.167	0	-1.6154	0.2643	0.0229	0.232	-0.3015	-0.1284	0.0199	-0.0421	0.0918	-0.1502	-0.0428	-0.0821	-0.0166	-0.0206	-0.0089	-0.0574	0.0094	23.9243	1.7827	-11.1019
16	4.9601	0.5317	0.7121	0.7714	0.0592	1.8652	-0.0567	-0.1724	-0.3018	0.0702	-0.0819	-0.1235	-0.061	-0.0834	0.1386	-0.0028	-0.0089	0.0023	-0.064	0.0015	0.015	33.9642	12.2986	-4.907
17	1.322	-2.3226	-0.0124	1.1559	-1.8577	0.0014	0.0075	-0.369	0.0973	0.0819	0.1362	0.0468	0.0358	-0.1232	-0.1437	-0.0415	-0.0396	0.0093	0.1386	-0.0484	-0.026	16.6188	8.5181	4.2969
18	3.8757	0.9341	0.6977	0.8196	0.1899	0.3263	-0.0225	-0.4344	-0.1136	0.0276	-0.0596	0.0107	-0.0261	-0.1068	0.0821	-0.0019	0.0119	0.0053	-0.0196	-0.0244	-0.0353	35.3321	21.529	0.8116
19	2.1436	3.1182	-0.145	0.4135	-1.017	2.4969	0.1294	-0.3146	-0.2321	0.0565	-0.1839	-0.2774	0.2902	0.0242	0.0545	0.0094	-0.0305	0.0155	-0.0226	0.003	-0.0661	26.7846	28.2821	16.7632
20	1.9162	-0.087	0.8844	1.2298	-0.4517	3.2907	0.0978	-0.6345	-0.1659	0.3069	-0.0178	0.0667	0.235	-0.4408	-0.08	-0.0979	-0.0845	-0.031	0.0094	0.0506	-0.1943	32.051	29.7663	32.9791
21	4.436	1.2827	1.3864	1.3044	-0.058	1.3822	0.1453	-0.2868	-0.0675	0.4842	0.1313	-0.4355	0.455	0.1734	-0.2766	-0.0839	0.0736	-0.1949	0.0126	-0.1555	-0.1202	50.9398	38.8258	37.1225
22	2.3916	0.9155	-1.6227	4.2455	2.9982	3.1827	0.0355	-0.0285	0.5133	0.0095	-0.1568	0.2447	0.004	0.0224	0.1213	-0.0507	-0.0479	-0.1789	0.1803	-0.1672	-0.0855	42.9403	49.7204	38.9494
23	0.8757	2.0251	1.1158	6.7392	2.9321	0.7195	-0.0109	0.0553	0.1701	0.0231	-0.0132	-0.0376	-0.1184	-0.0577	0.0241	-0.1177	0.0444	-0.1689	0.257	-0.0695	-0.1431	53.9943	52.6421	37.2364
24	0	1.5875	3.39	0.0021	2.9284	4.6849	-0.0083	0.0325	-0.0082	0.0475	0.0823	-0.2674	-0.0434	-0.0586	-0.074	-0.1269	0.0105	-0.1371	0.2565	-0.1318	-0.0825	56.221	48.1025	34.3272

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|-12 - 38}
2	X-RAY DIFFRACTION	2	{A\|39 - 96}
3	X-RAY DIFFRACTION	3	{A\|97 - 146}
4	X-RAY DIFFRACTION	4	{A\|147 - 199}
5	X-RAY DIFFRACTION	5	{A\|200 - 243}
6	X-RAY DIFFRACTION	6	{A\|244 - 335}
7	X-RAY DIFFRACTION	7	{A\|336 - 361}
8	X-RAY DIFFRACTION	8	{A\|362 - 388}
9	X-RAY DIFFRACTION	9	{A\|389 - 399}
10	X-RAY DIFFRACTION	10	{A\|400 - 448}
11	X-RAY DIFFRACTION	11	{A\|449 - 484}
12	X-RAY DIFFRACTION	12	{A\|485 - 510}
13	X-RAY DIFFRACTION	13	{B\|-13 - 47}
14	X-RAY DIFFRACTION	14	{B\|48 - 83}
15	X-RAY DIFFRACTION	15	{B\|84 - 100}
16	X-RAY DIFFRACTION	16	{B\|101 - 140}
17	X-RAY DIFFRACTION	17	{B\|141 - 159}
18	X-RAY DIFFRACTION	18	{B\|160 - 199}
19	X-RAY DIFFRACTION	19	{B\|200 - 232}
20	X-RAY DIFFRACTION	20	{B\|233 - 372}
21	X-RAY DIFFRACTION	21	{B\|373 - 425}
22	X-RAY DIFFRACTION	22	{B\|426 - 460}
23	X-RAY DIFFRACTION	23	{B\|461 - 486}
24	X-RAY DIFFRACTION	24	{B\|487 - 510}

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