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- PDB-5ahm: IMP-bound form of the DeltaCBS mutant of IMPDH from Pseudomonas a... -

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Open data

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Basic information

Entry

Database: PDB / ID: 5ahm

Title

IMP-bound form of the DeltaCBS mutant of IMPDH from Pseudomonas aeruginosa

Components

INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / CBS MODULE / DELETION MUTANT / ALLOSTERIC REGU NUCLEOTIDE METABOLISM

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
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.74 Å

Authors

Labesse, G. / Alexandre, T. / Gelin, M. / Haouz, A. / Munier-Lehmann, H.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystallographic Studies of Two Variants of Pseudomonas Aeruginosa Impdh with Impaired Allosteric Regulation
Authors: Labesse, G. / Alexandre, T. / Gelin, M. / Haouz, A. / Munier-Lehmann, H.

History

Deposition	Feb 6, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 9, 2015	Group: Database references
Revision 1.2	Sep 16, 2015	Group: Database references
Revision 1.3	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

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

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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	5ahm.cif.gz	284.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5ahm.ent.gz	230.1 KB	Display	PDB format
PDBx/mmJSON format	5ahm.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/ah/5ahm ftp://data.pdbj.org/pub/pdb/validation_reports/ah/5ahm	HTTPS FTP

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Related structure data

Related structure data	5ahlC 5ahnC 4dqwS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2cu0-3 5uqf-4 6dvh-2 6dvh-1 5ahl-1 1eep-3 6dvi-3 6dvi-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
Related items in Molecule of the Month	#140 - Aug 2011 Rhomboid Protease GlpG similarity (4)

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Assembly

Deposited unit

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

hetero molecules

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

1

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

hetero molecules

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

hetero molecules

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

hetero molecules

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE

hetero molecules

defined by author&software
338 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	103.600, 103.600, 158.400
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

Components on special symmetry positions

ID	Model	Components
1	1	A-2170- HOH
2	1	A-2212- HOH

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Components

#1: Protein	INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE / IMP DEHYDROGENASE / IMPD / IMPDH Mass: 41702.574 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-92,202-489 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXM5, IMP dehydrogenase
#2: Chemical	ChemComp-IMP / INOSINIC ACID / Inosinic acid Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₄O₈P
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	DELETION OF THE CBS MODULE (RESIDUES 93-201)

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Experimental details

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.9 Å³/Da / Density % sol: 34.5 % / Description: NONE
Crystal grow	Details: HEPES 0.1 M PH 7.5, NH4SO4 1.26 M

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98011 Å / Relative weight: 1
Reflection	Resolution: 1.75→43.34 Å / Num. obs: 152733 / % possible obs: 99.5 % / Observed criterion σ(I): 1.1 / Redundancy: 3.5 % / B_iso Wilson estimate: 0.2 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 13.1
Reflection shell	Resolution: 1.74→1.81 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 2.9 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DQW

Resolution: 1.74→43.3 Å / SU ML: 0.2 / σ(F): 1.1 / Phase error: 19.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1887	7724	5.1 %
R_work	0.1608	-	-
obs	0.1622	152733	91.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.74→43.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5119	0	71	571	5761

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5424
X-RAY DIFFRACTION	f_angle_d	1.109	7373
X-RAY DIFFRACTION	f_dihedral_angle_d	14.073	2024
X-RAY DIFFRACTION	f_chiral_restr	0.044	855
X-RAY DIFFRACTION	f_plane_restr	0.005	956

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 (%)
1.7499-1.7698	0.3114	240	0.2979	4664	X-RAY DIFFRACTION	88
1.7698-1.7906	0.2921	270	0.2758	4737	X-RAY DIFFRACTION	91
1.7906-1.8124	0.2897	226	0.2592	4723	X-RAY DIFFRACTION	90
1.8124-1.8354	0.3077	289	0.2517	4569	X-RAY DIFFRACTION	88
1.8354-1.8595	0.2458	220	0.2383	4429	X-RAY DIFFRACTION	83
1.8595-1.885	0.234	237	0.2213	4449	X-RAY DIFFRACTION	85
1.885-1.9119	0.2546	222	0.2187	4946	X-RAY DIFFRACTION	93
1.9119-1.9405	0.2684	248	0.2027	4835	X-RAY DIFFRACTION	93
1.9405-1.9708	0.2355	239	0.1931	4962	X-RAY DIFFRACTION	93
1.9708-2.0031	0.2217	285	0.1924	4911	X-RAY DIFFRACTION	93
2.0031-2.0377	0.2435	283	0.1884	4842	X-RAY DIFFRACTION	93
2.0377-2.0747	0.2123	292	0.1766	4945	X-RAY DIFFRACTION	93
2.0747-2.1146	0.1992	252	0.1698	4901	X-RAY DIFFRACTION	93
2.1146-2.1578	0.2227	277	0.1683	4882	X-RAY DIFFRACTION	93
2.1578-2.2047	0.1996	247	0.1587	4788	X-RAY DIFFRACTION	91
2.2047-2.256	0.1815	224	0.1611	4515	X-RAY DIFFRACTION	86
2.256-2.3124	0.1853	290	0.1635	4495	X-RAY DIFFRACTION	87
2.3124-2.3749	0.1983	251	0.1575	4956	X-RAY DIFFRACTION	95
2.3749-2.4448	0.1917	278	0.1611	4970	X-RAY DIFFRACTION	95
2.4448-2.5237	0.2039	278	0.1539	4996	X-RAY DIFFRACTION	95
2.5237-2.6139	0.1965	245	0.155	4935	X-RAY DIFFRACTION	94
2.6139-2.7185	0.1796	259	0.1558	5017	X-RAY DIFFRACTION	95
2.7185-2.8422	0.1845	294	0.1641	5001	X-RAY DIFFRACTION	95
2.8422-2.992	0.2112	245	0.1688	4609	X-RAY DIFFRACTION	88
2.992-3.1794	0.1876	263	0.164	4842	X-RAY DIFFRACTION	93
3.1794-3.4248	0.1745	288	0.1505	5064	X-RAY DIFFRACTION	96
3.4248-3.7693	0.1556	254	0.133	4976	X-RAY DIFFRACTION	95
3.7693-4.3143	0.1411	274	0.1232	5130	X-RAY DIFFRACTION	97
4.3143-5.4339	0.1672	205	0.1321	4886	X-RAY DIFFRACTION	93
5.4339-43.3579	0.1638	249	0.1682	5034	X-RAY DIFFRACTION	95

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	0.1447	-0.0251	-0.1105	0.0509	0.0386	0.0161	-0.0029	0.0212	-0.0141	0.0384	-0.0027	-0.0241	-0.0026	-0.0336	0	0.108	0.0028	0.0091	0.1057	0.0246	0.1401	-20.9283	-14.1125	4.9284
2	0.0016	-0.0067	0.0023	0.0061	0.013	0.0258	0.1213	0.2587	-0.1495	-0.0814	-0.1574	0.1359	0.013	0.0073	0	0.089	0.0236	-0.0469	0.1761	-0.0478	0.1912	-40.0548	-16.4005	-8.1522
3	0.0348	-0.0207	0.0248	0.14	0.0134	0.1042	0.0412	0.0071	0.0008	0.0342	-0.0285	0.0236	-0.0246	-0.0012	-0	0.0758	0.0045	0.0216	0.1011	0.0055	0.1495	-31.4612	-3.439	5.443
4	0.01	0.0143	-0.0035	0.0356	0.0107	0.0062	0.1133	0.0168	-0.0388	-0.0764	-0.0191	-0.0191	0.06	-0.0567	0	0.1499	0.0401	0.0225	0.144	0.0006	0.0835	-23.8873	-9.8103	-13.8736
5	0.0655	0.0353	0.0132	0.0107	0.0047	0.0241	-0.0209	0.0614	-0.0334	0.0089	0.0211	-0.0908	-0.091	-0.0019	-0	0.1501	0.0128	0.0303	0.1552	-0.0068	0.1243	-21.227	-12.0655	-8.5323
6	0.0261	-0.0405	0.0176	0.0086	-0.0042	-0.0125	-0.0327	0.111	0.0033	-0.0056	0.0497	-0.0527	0.1059	-0.0216	-0	0.0857	-0.001	0.0176	0.1398	0.0391	0.1138	-9.0262	-16.5982	0.2721
7	0.0593	0.0278	0.0399	0.1264	0.0353	0.0582	0.0233	-0.0205	0.0013	-0.0285	-0.0208	0.0344	0.0338	0.0144	0	0.16	-0.0126	-0.0409	0.1685	0.0043	0.1131	-15.9001	-19.7916	-53.2331
8	-0.0103	-0.0028	-0.0132	-0.0107	-0.0095	0.0105	-0.0503	-0.1333	-0.0081	0.1646	-0.1739	0.1869	0.1709	-0.0383	-0	0.3009	-0.1338	0.0244	-0.1105	0.5239	-0.1775	-17.979	-38.318	-39.4598
9	-0.0014	-0.0098	-0.02	0.0358	0.035	0.0205	0.0155	-0.0933	-0.1152	0.0219	0.025	-0.0108	0.1978	0.1002	-0	0.3029	-0.0107	-0.053	0.17	0.0178	0.2497	-8.0769	-41.3449	-51.0214
10	0.0534	0.0216	-0.0177	0.0149	-0.0689	0.0416	-0.0033	-0.0319	-0.0471	-0.0468	0.0577	-0.0018	-0.0086	-0.0137	-0	0.1935	-0.0176	-0.0338	0.1696	-0.0213	0.1217	-7.2476	-24.9259	-54.9577
11	0.0002	-0.0004	0.0071	0.0195	0.0041	-0.0009	0.0891	-0.2099	0.0238	-0.1087	0.0215	0.0583	-0.027	-0.0136	-0	0.1854	-0.0596	-0.0739	0.336	0.0218	-0.0267	-12.2467	-22.9565	-34.2663
12	0.003	-0.0038	0.0086	-0.0019	-0.0043	0.0052	0.0181	0.0042	-0.0058	0.0061	-0.0279	-0.0746	0.0126	0.0202	-0	0.3234	-0.0203	-0.0389	0.521	-0.0295	0.1986	-6.0821	-22.9993	-33.7435
13	0.0004	0.0026	0.0041	0.0027	0.0006	0.0008	-0.0374	-0.0562	0.0362	0.0168	-0.087	0.1062	0.006	-0.0525	0	0.2205	-0.0258	0.0081	0.2241	-0.0107	0.1806	-24.7314	-16.4849	-45.6058
14	0.0138	-0.0225	-0.011	0.0137	-0.009	-0.0046	0.0473	0.0251	-0.0321	0.1322	-0.073	0.1499	-0.063	-0.081	-0	0.243	-0.0093	-0.0143	0.1545	0.0114	0.0842	-17.45	-7.1377	-47.8408

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 1 THROUGH 54 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 55 THROUGH 217 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 218 THROUGH 352 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 353 THROUGH 385 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 386 THROUGH 447 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 448 THROUGH 487 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 1 THROUGH 54 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 55 THROUGH 210 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 211 THROUGH 266 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 267 THROUGH 352 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 353 THROUGH 385 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 386 THROUGH 428 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 429 THROUGH 447 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 448 THROUGH 487 )

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