PDB-8p37: Structure a catalytically inactive mutant of the IMP dehydrogenas...

ID or keywords:

Entry

Database: PDB / ID: 8p37

Title

Structure a catalytically inactive mutant of the IMP dehydrogenase related protein GUAB3 from Synechocystis PCC 6803

Components

IMP dehydrogenase subunit

Keywords

BIOSYNTHETIC PROTEIN / Complex of the enzyme with cofactor and product

Function / homology

Function and homology information

IMP dehydrogenase activity / purine nucleotide biosynthetic process
Similarity search - Function

Biological species

Synechocystis sp. PCC 6803 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.219 Å

Authors

Hernandez-Gomez, A. / Fernandez-Justel, D. / Buey, R.M.

Funding support

Spain, 1items

Citation

Journal: Structure / Year: 2023
Title: GuaB3, an overlooked enzyme in cyanobacteria's toolbox that sheds light on IMP dehydrogenase evolution.
Authors: Hernandez-Gomez, A. / Irisarri, I. / Fernandez-Justel, D. / Pelaez, R. / Jimenez, A. / Revuelta, J.L. / Balsera, M. / Buey, R.M.

History

Deposition	May 17, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8p37.cif.gz	222.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8p37.ent.gz	176.8 KB	Display	PDB format
PDBx/mmJSON format	8p37.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8p37_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	8p37_full_validation.pdf.gz	1.1 MB	Display
Data in XML	8p37_validation.xml.gz	18.8 KB	Display
Data in CIF	8p37_validation.cif.gz	28.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p3/8p37 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/8p37	HTTPS FTP

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Related structure data

Related structure data	8p4qC C: citing same article (ref.)
Similar structure data	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

Deposited unit

A: IMP dehydrogenase subunit

hetero molecules

41.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: IMP dehydrogenase subunit

hetero molecules

A: IMP dehydrogenase subunit

hetero molecules

A: IMP dehydrogenase subunit

hetero molecules

A: IMP dehydrogenase subunit

hetero molecules

defined by author
Evidence: gel filtration
166 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	112.867, 112.867, 54.119
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	79
Space group name H-M	I4

#1: Protein	IMP dehydrogenase subunit Mass: 40537.801 Da / Num. of mol.: 1 / Mutation: C222S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: guaB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73853
#2: Chemical	ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE Mass: 365.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₄O₉P
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.14 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop Details: SynGUAB3-C222S crystals were grown in the presence of IMP and NAD+ in mother liquor from the condition 2-48 of the commercial screen Morpheus (Molecular Dimensions), which consists of an ...Details: SynGUAB3-C222S crystals were grown in the presence of IMP and NAD+ in mother liquor from the condition 2-48 of the commercial screen Morpheus (Molecular Dimensions), which consists of an amino acid mixture (0.02M DL-Glutamic acid monohydrate, 0.02M DL-Alanine, 0.02M Glycine, 0.02M DL-Lysine monohydrochloride, and 0.02M DL-Serine, a precipitant mix (25% (v/v) PEG 500 MME and 12.5 % (w/v) PEG 20000), and 0.1M of a buffer system (Tris-base, Bicine) adjusted at pH 8.5. Initial conditions: Buffer: 10 mM TrisHCl, pH 8.0 Protein concentration = 15 mg/mL Substrate concentration: 3 mM NAD + 3 mM IMP

Crystal

Density Matthews: 2.13 Å³/Da / Density % sol: 42.14 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop
Details: SynGUAB3-C222S crystals were grown in the presence of IMP and NAD+ in mother liquor from the condition 2-48 of the commercial screen Morpheus (Molecular Dimensions), which consists of an ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALBA

/ Beamline: XALOC / Wavelength: 0.979181423454 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979181423454 Å / Relative weight: 1

Reflection

Resolution: 1.219→39.905 Å / Num. obs: 77746 / % possible obs: 94 % / Redundancy: 12.82 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC_1/2: 0.999 / CC_1/2 anomalous: -0.339 / R_merge(I) obs: 0.0877 / R_pim(I) all: 0.0254 / R_rim(I) all: 0.0914 / AbsDiff over sigma anomalous: 0.71 / B_aniso tensor eigenvalue 1: 0 Å² / B_aniso tensor eigenvalue 2: 0 Å² / B_aniso tensor eigenvalue 3: 9.4753 Å² / B_aniso tensor eigenvector 1 ortho1: 1 / B_aniso tensor eigenvector 1 ortho2: 0 / B_aniso tensor eigenvector 1 ortho3: 0 / B_aniso tensor eigenvector 2 ortho1: 0 / B_aniso tensor eigenvector 2 ortho2: 1 / B_aniso tensor eigenvector 2 ortho3: 0 / B_aniso tensor eigenvector 3 ortho1: 0 / B_aniso tensor eigenvector 3 ortho2: 0 / B_aniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 1.219 Å / Aniso diffraction limit 2: 1.219 Å / Aniso diffraction limit 3: 1.506 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 14.54 / Num. measured all: 996816 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 93.8 / % possible ellipsoidal: 94 / % possible ellipsoidal anomalous: 93.8 / % possible spherical: 76.7 / % possible spherical anomalous: 75.9 / Redundancy anomalous: 6.55 / Signal type: local

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
3.652-39.905	12.61	0.0428	53.3	48957	48957	3883	3883	0.999	-0.444	0.0124	0.0446	0.539	99.8	99.8	99.8	99.8	99.8	6.62	99.8
2.889-3.652	12.07	0.0473	45.21	46953	46953	3890	3890	0.999	-0.348	0.0139	0.0493	0.704	99.8	99.8	99.8	99.8	99.8	6.22	99.8
2.521-2.889	12.77	0.0608	36.95	49648	49648	3888	3888	0.999	-0.183	0.0177	0.0633	0.786	99.8	99.8	99.8	99.8	99.8	6.54	99.8
2.286-2.521	13.56	0.076	31.11	52725	52725	3887	3887	0.998	-0.204	0.0214	0.079	0.741	99.8	99.8	99.8	99.8	99.8	6.94	99.8
2.121-2.286	13.89	0.0941	26.34	54023	54023	3888	3888	0.998	-0.205	0.0263	0.0978	0.77	99.8	99.8	99.8	99.8	99.8	7.1	99.8
1.995-2.121	12.68	0.1237	20.4	49296	49296	3888	3888	0.997	-0.134	0.036	0.1289	0.756	100	100	100	100	100	6.45	100
1.895-1.995	13.21	0.1699	15.67	51332	51332	3887	3887	0.995	-0.094	0.0485	0.1767	0.725	100	100	100	100	100	6.72	100
1.812-1.895	13.24	0.2234	12.07	51414	51414	3883	3883	0.992	-0.082	0.0638	0.2324	0.73	100	100	100	100	100	6.73	100
1.741-1.812	12.35	0.2875	9.31	48063	48063	3891	3891	0.987	-0.053	0.0851	0.3	0.714	100	100	100	100	100	6.26	100
1.681-1.741	13.09	0.4	7.03	50899	50899	3889	3889	0.976	-0.032	0.1148	0.4164	0.72	100	100	100	100	100	6.64	100
1.628-1.681	13.45	0.4538	6.28	52288	52288	3887	3887	0.971	0.015	0.1286	0.4719	0.73	100	100	100	100	100	6.82	100
1.581-1.628	13.48	0.527	5.32	52427	52427	3888	3888	0.96	-0.006	0.1492	0.5479	0.702	99.8	99.8	99.8	99.8	99.8	6.84	99.8
1.539-1.581	13.47	0.6281	4.48	52311	52311	3883	3883	0.947	-0.004	0.1779	0.653	0.699	99.1	99.2	99.1	99.2	99.1	6.82	99.2
1.5-1.539	13.38	0.7257	3.82	52021	52021	3889	3889	0.931	-0.019	0.2063	0.7547	0.715	96.2	96.3	96.2	96	95.9	6.78	96.3
1.462-1.5	12.19	0.8629	3.02	47368	47368	3885	3885	0.895	-0.012	0.2572	0.9009	0.712	95.3	95.5	95.3	90.8	90.5	6.18	95.5
1.423-1.462	12.12	0.9862	2.59	47121	47121	3888	3888	0.847	-0.03	0.2947	1.0299	0.692	89	89.4	89	78.7	78.1	6.17	89.4
1.379-1.423	12.88	1.0071	2.58	50120	50120	3890	3890	0.854	0.002	0.2912	1.0488	0.707	78.8	79.5	78.8	62.4	61.5	6.56	79.5
1.333-1.379	11.76	1.2432	1.97	45713	45713	3886	3886	0.784	-0.031	0.3766	1.2999	0.686	75.3	76.2	75.3	51.1	49.9	6.02	76.2
1.284-1.333	12.29	1.3047	1.87	47822	47822	3890	3890	0.757	-0.001	0.385	1.3613	0.689	78.4	79.3	78.4	42.8	41.4	6.33	79.3
1.219-1.284	11.92	1.558	1.51	46315	46315	3886	3886	0.68	-0.031	0.4665	1.6279	0.668	80	80.1	80	26.6	25.3	6.18	80.1

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Processing

Software

Name	Version	Classification
BUSTER	2.10.4	refinement
autoPROC	1.0.5 20220608	data processing
autoPROC	Jan 10, 2022	data processing
Aimless	0.7.9	data scaling
autoPROC	2.3.87	data processing
XDS	20220820	data reduction
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.219→39.91 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.953 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.053 / SU R_free Blow DPI: 0.052 / SU R_free Cruickshank DPI: 0.05

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1876	3882	-	RANDOM
R_work	0.1749	-	-	-
obs	0.1755	77746	76.7 %	-

Displacement parameters

B_iso mean: 16.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.2698 Å²	0 Å²	0 Å²
2-	-	0.2698 Å²	0 Å²
3-	-	-	-0.5396 Å²

Refine analyze

Luzzati coordinate error obs: 0.15 Å

Refinement step

Cycle: LAST / Resolution: 1.219→39.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2753	0	68	331	3152

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.013	5759	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.29	10490	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1737	SINUSOIDAL	2
X-RAY DIFFRACTION	t_gen_planes		891	HARMONIC	5
X-RAY DIFFRACTION	t_it		5759	HARMONIC	10
X-RAY DIFFRACTION	t_chiral_improper_torsion		412	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact		6667	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_omega_torsion	4.9
X-RAY DIFFRACTION	t_other_torsion	13.46

LS refinement shell

Resolution: 1.22→1.25 Å

	R_factor	Num. reflection	% reflection
R_free	0.2395	65	-
R_work	0.2323	-	-
obs	0.2326	1555	20.36 %

Refinement TLS params.

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	0.237	0.0973	0.1055	1.6426	-0.1027	0.1897	0.0283	-0.1163	-0.0091	-0.1163	-0.0606	0.0221	-0.0091	0.0221	0.0323	0.1085	0.0046	0.0096	0.1168	-0.003	0.1245	8.9054	-6.6618	-30.9398
2	0.6599	-0.0006	0.0968	0.8772	0.1286	0.6534	-0.006	0.1009	-0.0262	0.1009	0.0224	0.0642	-0.0262	0.0642	-0.0164	0.0949	0.0043	-0.0056	0.1056	0.0131	0.1062	31.9653	-10.0643	-9.4724
3	0.7211	-0.3581	0.4573	0.8406	-0.3444	0.6714	0.0167	0.0699	-0.0077	0.0699	-0.0435	0.0987	-0.0077	0.0987	0.0268	0.0985	0.0021	-0.0073	0.1269	0.0173	0.1594	42.788	-12.0666	-11.6125
4	0.292	-0.1804	0.2186	1.8795	-0.7018	0.4622	0.0524	-0.0806	-0.0301	-0.0806	-0.1323	0.1026	-0.0301	0.1026	0.0799	0.1104	-0.003	0.0169	0.143	0.0065	0.1745	39.8788	-1.9702	-21.6978
5	0.3646	-0.0375	0.0893	0.6018	0.0414	0.3683	-0.0089	-0.0476	-0.0081	-0.0476	0.0018	0.0456	-0.0081	0.0456	0.007	0.0889	0.0011	0.0127	0.0971	0.0086	0.1004	27.2853	-5.5859	-23.3361
6	0.4996	0.1723	0.2913	0.6852	0.1222	0.4299	0.0315	0.0532	0.0406	0.0532	-0.005	-0.0376	0.0406	-0.0376	-0.0266	0.0886	0.0053	0.0075	0.0969	0.0086	0.1046	17.3688	-21.1154	-15.6373
7	0.4318	0.1158	-0.7506	0.2072	-0.2008	1.2747	0.0398	0.0519	-0.1068	0.0519	-0.0492	0.0491	-0.1068	0.0491	0.0094	0.1203	-0.0048	0.0059	0.1276	-0.0125	0.132	1.6017	-12.8264	-16.2999

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|2 - A\|30 }	A	2 - 30
2	X-RAY DIFFRACTION	2	{ A\|31 - A\|115 }	A	31 - 115
3	X-RAY DIFFRACTION	3	{ A\|116 - A\|138 }	A	116 - 138
4	X-RAY DIFFRACTION	4	{ A\|139 - A\|170 }	A	139 - 170
5	X-RAY DIFFRACTION	5	{ A\|171 - A\|313 }	A	171 - 313
6	X-RAY DIFFRACTION	6	{ A\|314 - A\|361 }	A	314 - 361
7	X-RAY DIFFRACTION	7	{ A\|362 - A\|386 }	A	362 - 386

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