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Yorodumi- PDB-7qu9: Structure of aminodeoxychorismate synthase component 1 (PabB) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qu9 | ||||||
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Title | Structure of aminodeoxychorismate synthase component 1 (PabB) from Bacillus subtilis spizizenii. | ||||||
Components | Anthranilate synthase component I family protein | ||||||
Keywords | TRANSFERASE / Chorismate / Magnesium / Folate | ||||||
Function / homology | Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / cellular biosynthetic process / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / TRYPTOPHAN / Anthranilate synthase component I family protein Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Rooms, L.D. / Race, P.R. / Back, C.B. / Burton, N.B. / Willis, C.L. / Stach, J.E.M. / Duke, P.W. / Hawkins, C. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structure of aminodeoxychorismate synthase component 1 (PabB) from Bacillus subtilis spizizenii. Authors: Rooms, L.D. / Race, P.R. / Back, C.B. / Burton, N.B. / Willis, C.L. / Stach, J.E.M. / Duke, P.W. / Hawkins, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qu9.cif.gz | 561.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qu9.ent.gz | 468.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/7qu9 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7qu9 | HTTPS FTP |
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-Related structure data
Related structure data | 5cwaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 53281.008 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: FAL52_19525 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5F2KFW0 #2: Chemical | #3: Chemical | #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: 2.45 Å3/Da / Density % sol: 49.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.04 M potassium phosphate monobasic, 16 % (w/v) PEG8000, 20 % (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.14→91.49 Å / Num. obs: 85192 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.049 / Rrim(I) all: 0.126 / Net I/σ(I): 7 / Num. measured all: 559025 / Scaling rejects: 1410 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CWA Resolution: 2.14→77.79 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2335 / WRfactor Rwork: 0.197 / FOM work R set: 0.7446 / SU B: 18.123 / SU ML: 0.209 / SU R Cruickshank DPI: 0.2343 / SU Rfree: 0.1827 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.48 Å2 / Biso mean: 64.548 Å2 / Biso min: 31.07 Å2
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Refinement step | Cycle: final / Resolution: 2.14→77.79 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.14→2.194 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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