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Yorodumi- PDB-8p37: Structure a catalytically inactive mutant of the IMP dehydrogenas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p37 | ||||||
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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 / nucleotide binding 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
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p37.cif.gz | 222.8 KB | Display | PDBx/mmCIF format |
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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 |
-Validation report
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.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-XMP / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-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 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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! CC1/2: 0.999 / CC1/2 anomalous: -0.339 / Rmerge(I) obs: 0.0877 / Rpim(I) all: 0.0254 / Rrim(I) all: 0.0914 / AbsDiff over sigma anomalous: 0.71 / Baniso tensor eigenvalue 1: 0 Å2 / Baniso tensor eigenvalue 2: 0 Å2 / Baniso tensor eigenvalue 3: 9.4753 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso 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 |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.219→39.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.05
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Displacement parameters | Biso mean: 16.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.219→39.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.25 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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