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Open data
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Basic information
Entry | Database: PDB / ID: 7oj2 | ||||||
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Title | Bacillus subtilis IMPDH in complex with Ap4A | ||||||
![]() | Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase | ||||||
![]() | SIGNALING PROTEIN / IMP Dehydrogenase / Delta CBS mutant | ||||||
Function / homology | ![]() IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Giammarinaro, P.I. / Bange, G. | ||||||
![]() | ![]() Title: Diadenosine tetraphosphate regulates biosynthesis of GTP in Bacillus subtilis. Authors: Giammarinaro, P.I. / Young, M.K.M. / Steinchen, W. / Mais, C.N. / Hochberg, G. / Yang, J. / Stevenson, D.M. / Amador-Noguez, D. / Paulus, A. / Wang, J.D. / Bange, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 63 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.1 KB | Display | ![]() |
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Full document | ![]() | 448.9 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oj1C ![]() 4dqwS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41199.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: guaB, gnaB, BSU00090 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-PO4 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.98 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M citrate pH 5.6, 0.2 M Potassium/Sodium tartrate, 2.0 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 29, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.76→55.46 Å / Num. obs: 48597 / % possible obs: 100 % / Redundancy: 24.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.037 / Rrim(I) all: 0.187 / Net I/σ(I): 13.4 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4DQW Resolution: 1.76→55.46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.047 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.67 Å2 / Biso mean: 27.109 Å2 / Biso min: 12.5 Å2
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Refinement step | Cycle: final / Resolution: 1.76→55.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.806 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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