+Open data
-Basic information
Entry | Database: PDB / ID: 8k4r | ||||||
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Title | Structure of VinM-VinL complex | ||||||
Components |
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Keywords | LIGASE / Complex / Adenylation enzyme / ATP / Carrier protein / Biosynthesis | ||||||
Function / homology | Function and homology information D-alanine:D-alanyl carrier protein ligase-like / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site ...D-alanine:D-alanyl carrier protein ligase-like / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain Similarity search - Domain/homology | ||||||
Biological species | Streptomyces halstedii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Miyanaga, A. / Nagata, K. / Nakajima, J. / Chisuga, T. / Kudo, F. / Eguchi, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Structural Basis of Amide-Forming Adenylation Enzyme VinM in Vicenistatin Biosynthesis. Authors: Miyanaga, A. / Nagata, K. / Nakajima, J. / Chisuga, T. / Kudo, F. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k4r.cif.gz | 429.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k4r.ent.gz | 350.3 KB | Display | PDB format |
PDBx/mmJSON format | 8k4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k4r_validation.pdf.gz | 844.9 KB | Display | wwPDB validaton report |
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Full document | 8k4r_full_validation.pdf.gz | 860.7 KB | Display | |
Data in XML | 8k4r_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 8k4r_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/8k4r ftp://data.pdbj.org/pub/pdb/validation_reports/k4/8k4r | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 58061.473 Da / Num. of mol.: 2 / Mutation: D223C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinM / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY3 #2: Protein | Mass: 11788.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinL / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY4 #3: Chemical | #4: Chemical | #5: 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: 46.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES-Na, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2022 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 54087 / % possible obs: 97.9 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4443 / CC1/2: 0.826 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 22.685 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 117.73 Å2 / Biso mean: 62.016 Å2 / Biso min: 33.47 Å2
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Refinement step | Cycle: final / Resolution: 2.3→46.04 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: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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