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Yorodumi- PDB-7wuo: Unravelling structure of riboflavin synthase for designing of pot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wuo | ||||||
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Title | Unravelling structure of riboflavin synthase for designing of potential anti-bacterial drug | ||||||
Components | Riboflavin synthase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / riboflavin / antibacterial | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Leptospira kmetyi serovar Malaysia str. Bejo-Iso9 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å | ||||||
Authors | Aris, S.N.A.M. / Leow, A.T.C. / Motomura, T. / Jonet, M.A. | ||||||
Funding support | Malaysia, 1items
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Citation | Journal: J.Mol.Struct. / Year: 2022 Title: Unraveling the crystal structure of Leptospira kmetyi riboflavin synthase and computational analyses for potential development of new antibacterials Authors: Aris, S.N.A.M. / Rahman, R.N.Z.R.A. / Ali, M.S.M. / Jonet, M.A. / Motomura, T. / Noor, N.D.M. / Shariff, F.M. / Hsu, K.C. / Chor, L.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wuo.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wuo.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 7wuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wuo_validation.pdf.gz | 907.5 KB | Display | wwPDB validaton report |
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Full document | 7wuo_full_validation.pdf.gz | 903.2 KB | Display | |
Data in XML | 7wuo_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 7wuo_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/7wuo ftp://data.pdbj.org/pub/pdb/validation_reports/wu/7wuo | HTTPS FTP |
-Related structure data
Related structure data | 1i8dS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 201 / Label seq-ID: 1 - 201
NCS ensembles :
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-Components
#1: Protein | Mass: 23227.416 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira kmetyi serovar Malaysia str. Bejo-Iso9 (bacteria) Gene: EHQ67_13285 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7I0ICZ8, riboflavin synthase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Nonpolymer details | The ligand should be polyethyleneglycol, because polyethyleneglycol has been used in both ...The ligand should be polyethyleneglycol, because polyethyleneglycol has been used in both crystallization formulation and as a cryoprotectant. | |
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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: 2.94 Å3/Da / Density % sol: 58.24 % / Description: Bullet shape |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M Ammonium Sulfate, 0.1M MES monohydrate (pH 6.5), 10% w/v PEG MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU / Detector: PIXEL / Date: Apr 19, 2019 / Details: dextris 200k |
Radiation | Monochromator: cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.19→40 Å / Num. obs: 13224 / % possible obs: 97.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1259 / CC1/2: 0.818 / % possible all: 99.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I8D Resolution: 3.19→27.26 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.844 / SU B: 24.531 / SU ML: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.526 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.34 Å2 / Biso mean: 39.875 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 3.19→27.26 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: 3.193→3.275 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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