PDB-4avf: Crystal structure of Pseudomonas aeruginosa inosine 5'-monophosph...

ID or keywords:

Entry

Database: PDB / ID: 4avf

Title

Crystal structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase

Components

INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE

Function / homology

Function and homology information

IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / ATP binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.23 Å

Authors

McMahon, S.A. / Moynie, L. / Liu, H. / Duthie, F. / Naismith, J.H.

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery
Authors: Moynie, L. / Schnell, R. / Mcmahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M.S. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...

History

Deposition	May 25, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jan 23, 2013	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4avf.cif.gz	473.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4avf.ent.gz	389 KB	Display	PDB format
PDBx/mmJSON format	4avf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4avf_validation.pdf.gz	440.7 KB	Display	wwPDB validaton report
Full document	4avf_full_validation.pdf.gz	444.4 KB	Display
Data in XML	4avf_validation.xml.gz	44.4 KB	Display
Data in CIF	4avf_validation.cif.gz	64.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/av/4avf ftp://data.pdbj.org/pub/pdb/validation_reports/av/4avf	HTTPS FTP

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Related structure data

Related structure data	2xu8C 4avrC 4avyC 4b79C 4b7cC 4b7xC 4b9aC 4b9eC 4es6C 4etrC 4exaC 4exbC 1vrdS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1eep-1 1eep-2 4fez-1 3ffs-d 1ak5-1 1mei-1 1me9-1 4mjm-d 1vrd-1 4fez-2 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
Related items in Molecule of the Month	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4)

Deposited unit

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

C: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

D: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

207 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	116.590, 116.590, 259.170
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE Mass: 51824.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9HXM5, IMP dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

Mass: 51824.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: Q9HXM5, IMP dehydrogenase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.14 Å³/Da / Density % sol: 42.2 % / Description: NONE
Crystal grow	pH: 6.5 / Details: 11% PEG 4000, 0.1M MES PH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2010 / Details: MIRRORS
Radiation	Monochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 2.23→106 Å / Num. obs: 87734 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / R_merge(I) obs: 0.08 / Net I/σ(I): 18.5
Reflection shell	Resolution: 2.23→2.29 Å / Redundancy: 9.4 % / R_merge(I) obs: 0.75 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.6.0117	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VRD

1vrd

Resolution: 2.23→106.33 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.956 / SU B: 8.762 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED DISORDERED. RESIDUES 91-204 AND 385-420. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20003	4397	5 %	RANDOM
R_work	0.17942	-	-	-
obs	0.18045	83337	99.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 52.371 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.42 Å²	0 Å²	0 Å²
2-	-	-0.42 Å²	0 Å²
3-	-	-	0.85 Å²

Refinement step

Cycle: LAST / Resolution: 2.23→106.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9094	0	0	360	9454

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	9212
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	6131
X-RAY DIFFRACTION	r_angle_refined_deg	1.242	1.968	12455
X-RAY DIFFRACTION	r_angle_other_deg	1.081	3	15010
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.617	5	1249
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.414	23.82	322
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.34	15	1540
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.574	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	1481
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	10381
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1745
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.23→2.287 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.27	279	-
R_work	0.241	5689	-
obs	-	-	99.98 %

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	0.1832	0.1643	0.1881	0.35	-0.1427	0.716	-0.0109	0.0365	-0.0818	-0.0277	0.03	-0.0794	0.0258	-0.0245	-0.0191	0.1888	0.0506	0.044	0.2027	-0.01	0.1915	0.991	-16.6115	31.2102
2	1.8783	0.0971	-0.0594	0.7126	-0.0922	0.8514	0.0869	0.0569	0.1096	0.0043	0.0841	-0.1959	-0.0824	0.1091	-0.1711	0.1866	-0.0175	0.1406	0.1947	-0.0388	0.1879	19.4476	0.3519	25.0338
3	3.6143	0.1554	-1.6016	0.9555	-0.3183	1.3859	0.1528	0.241	0.0753	-0.0846	0.0331	-0.0064	-0.1597	-0.0923	-0.1858	0.2467	0.0547	0.1014	0.2563	0.0598	0.0714	3.1064	0.4475	16.1318
4	4.16	5.402	0.4717	7.2396	0.645	0.0584	0.3575	-0.1294	-0.4249	0.3035	-0.2619	-0.9353	0.0146	-0.0361	-0.0955	0.2348	0.126	0.2105	0.221	0.2096	0.7043	-6.5143	4.4847	36.0509
5	0.6367	0.4953	-0.424	1.5331	-1.9291	2.5632	0.1275	0.0699	-0.1963	0.0728	0.0154	-0.0271	-0.0974	-0.0531	-0.1429	0.1762	0.0558	0.0487	0.2214	0.0126	0.223	0.7562	-10.6533	29.1079
6	3.3049	-1.1142	4.6284	1.7558	0.3354	9.1136	-0.381	-0.7113	0.2029	0.0285	0.4384	-0.3382	-0.6013	-0.7712	-0.0574	0.2032	-0.0218	0.0632	0.3628	-0.1339	0.1338	17.38	3.309	45.9479
7	1.4144	0.5533	-0.4761	1.0872	-0.3911	1.1252	0.0361	0.0168	-0.2324	-0.0217	0.0153	-0.1048	0.0812	0.0706	-0.0514	0.16	0.0203	0.0199	0.1926	-0.0129	0.1718	4.7917	-19.1816	35.8914
8	1.0727	-0.0589	0.029	0.3258	0.2154	0.1816	0.0276	0.0472	-0.0603	-0.2239	-0.1303	0.0825	-0.0902	-0.0284	0.1027	0.2813	0.1274	0.014	0.2418	0.0847	0.1141	-20.962	7.9647	29.5279
9	0.995	0.1552	-0.5781	2.6174	-0.1688	0.4092	0.146	-0.2601	0.085	-0.1095	-0.2165	0.3006	-0.0954	0.2018	0.0706	0.1503	0.0258	-0.0562	0.2282	-0.0089	0.2466	-29.5092	30.91	38.4649
10	1.2762	-1.4806	-0.1719	5.665	-1.1686	0.5113	0.0613	-0.1517	-0.1352	-0.1528	-0.0257	0.5134	0.0059	0.1086	-0.0356	0.0973	0.0748	-0.1309	0.1844	0.0127	0.3272	-40.0912	16.4493	36.4009
11	0.5647	-0.2207	-0.2435	1.9515	0.088	0.1074	0.0387	-0.1964	-0.0307	-0.2681	-0.0697	0.1403	-0.0036	0.1037	0.031	0.1614	0.0713	-0.0164	0.2561	0.0712	0.158	-26.2715	8.637	37.0205
12	2.8786	2.6475	0.1892	5.0171	4.2213	6.4528	0.4935	-0.8322	-0.2331	0.5978	-0.5179	-0.1773	0.3464	0.4249	0.0244	0.1807	-0.0756	-0.0629	0.4483	0.116	0.166	-14.0691	25.9356	49.8491
13	4.2968	5.0856	0.9514	13.4209	11.6856	15.2795	0.432	-0.3835	-0.3274	0.1906	-0.4214	-0.4211	-0.2174	-0.1383	-0.0106	0.1427	0.0086	0.0007	0.2583	0.246	0.2357	-11.5639	17.6217	33.3827
14	1.1791	-1.3907	-0.0942	2.4464	0.4338	1.8196	0.0834	0.1083	-0.1238	-0.4564	-0.0727	-0.0825	-0.0548	0.0127	-0.0107	0.2403	0.0728	0.0829	0.2539	0.0424	0.1415	-15.8608	6.0199	26.8001
15	0.7474	-0.1606	-0.4488	0.4212	0.0937	0.5725	-0.0303	0.1072	-0.1039	0.137	-0.0194	0.0298	0.0883	-0.0668	0.0497	0.2192	-0.0232	0.0081	0.1101	0.0105	0.2055	-14.2892	-32.2107	56.2048
16	2.8521	-0.2675	-0.8057	0.7777	0.0176	1.7122	-0.1884	-0.2457	-0.1952	0.1598	0.0573	-0.1125	0.1595	0.1983	0.1311	0.2562	0.0918	-0.0309	0.1049	0.1094	0.2259	4.9667	-42.4654	64.4516
17	1.9518	-1.3505	-0.3478	3.8596	-1.9505	1.7108	-0.0816	0.1307	-0.0778	-0.0562	-0.1227	-0.1622	0.1241	-0.0085	0.2043	0.2416	0.0054	0.0155	0.0873	-0.0023	0.2363	1.4919	-40.9511	45.987
18	10.5811	4.4074	1.135	1.8602	0.0329	8.2659	-0.0417	-0.9673	-0.1574	-0.0072	-0.4321	-0.0934	-0.2006	-0.0491	0.4738	0.355	0.0916	0.0052	0.2359	0.0241	0.1541	0.2689	-18.4353	47.5694
19	2.443	-1.2799	-0.9838	0.9463	0.0357	1.3004	-0.0265	0.0539	0.0335	0.0523	0.0132	-0.0559	0.02	-0.1754	0.0132	0.2154	-0.0226	-0.0031	0.1356	0.0051	0.2221	-11.8513	-31.5812	51.6761
20	1.0472	1.0627	0.0976	1.6328	1.4688	3.515	0.2103	-0.0141	-0.0935	0.0241	0.131	-0.1707	-0.3761	0.3893	-0.3413	0.3713	-0.001	-0.0774	0.1563	-0.0212	0.1744	0.3575	-24.0182	72.0614
21	2.3602	-1.4593	0.033	3.7276	-0.2538	0.4513	-0.0373	0.0851	-0.2512	0.0714	-0.0838	0.0789	0.0861	-0.2649	0.1212	0.1854	-0.0346	0.0332	0.185	-0.0411	0.2023	-22.6566	-30.2747	57.0649
22	0.0464	-0.0153	0.0898	1.7608	-0.714	0.5934	0.0416	0.0658	0.0317	-0.0815	0.0251	0.2563	0.0589	-0.0348	-0.0667	0.0736	0.0592	0.0422	0.2557	0.0433	0.2887	-39.226	-6.7138	51.7307
23	0.6754	0.4085	0.1765	2.6613	-0.6736	1.1343	0.2765	0.1008	0.1541	0.6168	-0.0015	0.4288	-0.1762	0.0136	-0.2751	0.3412	-0.0245	0.2896	0.0821	-0.0296	0.2808	-45.6148	-7.9426	76.2596
24	0.8987	1.3004	-1.689	7.2405	-1.8987	3.268	0.0874	-0.072	0.0815	0.3733	-0.0348	0.2954	0.021	0.1623	-0.0525	0.3124	-0.0023	0.1984	0.1212	0.0435	0.2592	-44.8323	-21.4221	76.8386
25	2.6584	0.0403	-1.8403	1.7024	-1.4092	2.5518	0.0384	0.0487	0.0187	0.0268	0.0998	0.2011	0.1048	-0.0037	-0.1382	0.2183	-0.0074	0.0612	0.1752	-0.0154	0.2512	-41.8543	-24.4317	64.3595
26	0.1007	-0.3085	0.0477	1.676	-0.8035	0.6824	0.0135	0.0397	0.0437	0.0655	0.0304	0.0209	0.0104	-0.0559	-0.0439	0.1363	0.0001	0.0695	0.2007	-0.0001	0.2712	-35.3321	-13.1641	56.7319
27	2.0502	0.2162	2.5304	3.2828	2.2586	4.3545	0.0609	0.1416	0.0736	0.5169	0.101	-0.3933	0.3495	0.1907	-0.1619	0.3851	-0.0647	0.2013	0.1146	-0.061	0.2806	-30.6064	0.84	75.4728
28	1.599	-0.0517	-1.1834	2.0516	-1.6022	2.2132	0.1736	0.1088	-0.0689	-0.1168	0.044	0.3982	-0.0516	-0.0719	-0.2175	0.0849	0.0086	0.0057	0.2007	0.0457	0.283	-39.6789	-1.508	49.307

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 39
2	X-RAY DIFFRACTION	2	A	40 - 245
3	X-RAY DIFFRACTION	3	A	246 - 298
4	X-RAY DIFFRACTION	4	A	299 - 313
5	X-RAY DIFFRACTION	5	A	314 - 358
6	X-RAY DIFFRACTION	6	A	359 - 428
7	X-RAY DIFFRACTION	7	A	429 - 467
8	X-RAY DIFFRACTION	8	B	1 - 39
9	X-RAY DIFFRACTION	9	B	40 - 245
10	X-RAY DIFFRACTION	10	B	246 - 302
11	X-RAY DIFFRACTION	11	B	303 - 357
12	X-RAY DIFFRACTION	12	B	358 - 434
13	X-RAY DIFFRACTION	13	B	435 - 440
14	X-RAY DIFFRACTION	14	B	441 - 468
15	X-RAY DIFFRACTION	15	C	1 - 52
16	X-RAY DIFFRACTION	16	C	53 - 245
17	X-RAY DIFFRACTION	17	C	246 - 298
18	X-RAY DIFFRACTION	18	C	299 - 312
19	X-RAY DIFFRACTION	19	C	313 - 356
20	X-RAY DIFFRACTION	20	C	357 - 436
21	X-RAY DIFFRACTION	21	C	437 - 467
22	X-RAY DIFFRACTION	22	D	1 - 38
23	X-RAY DIFFRACTION	23	D	39 - 218
24	X-RAY DIFFRACTION	24	D	219 - 247
25	X-RAY DIFFRACTION	25	D	248 - 304
26	X-RAY DIFFRACTION	26	D	305 - 356
27	X-RAY DIFFRACTION	27	D	357 - 436
28	X-RAY DIFFRACTION	28	D	437 - 468

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