+Open data
-Basic information
Entry | Database: PDB / ID: 7pi1 | ||||||
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Title | Bacillus subtilis PabB | ||||||
Components | Aminodeoxychorismate synthase component 1 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information aminodeoxychorismate synthase / 4-amino-4-deoxychorismate synthase activity / folic acid biosynthetic process / tryptophan biosynthetic process / tetrahydrofolate biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.729 Å | ||||||
Authors | Rooms, L.D. / Race, P.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To be published Title: Crystal structure of Bacillus subtilis PabB, component 1. Authors: Rooms, L.D. / Race, P.R. / Devine, A. / Willis, C.L. / Back, C.R. / Burton, N. / Sudol, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pi1.cif.gz | 689.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pi1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pi1_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7pi1_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7pi1_validation.xml.gz | 73.9 KB | Display | |
Data in CIF | 7pi1_validation.cif.gz | 107.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pi/7pi1 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/7pi1 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 55464.406 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: pabB, pab, BSU00740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P28820, aminodeoxychorismate synthase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TRP / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.06 M magnesium chloride hexahydrate, 0.06 M calcium chloride dihydrate, 20 % v/v PEG 500 MME, 10 % w/v PEG 20000, 0.01 M tris (base); BICINE, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.729→51.08 Å / Num. obs: 206370 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 22.91 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.094 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 1.729→1.76 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 10035 / CC1/2: 0.256 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model used not yet deposited Resolution: 1.729→50.826 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.118
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.435 Å2
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Refinement step | Cycle: LAST / Resolution: 1.729→50.826 Å
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Refine LS restraints |
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LS refinement shell |
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