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Yorodumi- PDB-7dq6: Crystal structure of HitB in complex with (S)-beta-3-Br-phenylala... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dq6 | ||||||
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Title | Crystal structure of HitB in complex with (S)-beta-3-Br-phenylalanine sulfamoyladenosine | ||||||
Components | Putative ATP-dependent b-aminoacyl-ACP synthetase | ||||||
Keywords | LIGASE / Hitachimycin / Polyketide biosynthesis / ATP binding / Adenylation | ||||||
Function / homology | Function and homology information AMP-binding / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-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 Similarity search - Domain/homology | ||||||
Biological species | Embleya scabrispora (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Kudo, F. / Takahashi, S. / Miyanaga, A. / Nakazawa, Y. / Eguchi, T. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Mutational Biosynthesis of Hitachimycin Analogs Controlled by the beta-Amino Acid-Selective Adenylation Enzyme HitB. Authors: Kudo, F. / Takahashi, S. / Miyanaga, A. / Nakazawa, Y. / Nishino, K. / Hayakawa, Y. / Kawamura, K. / Ishikawa, F. / Tanabe, G. / Iwai, N. / Nagumo, Y. / Usui, T. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dq6.cif.gz | 363.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dq6.ent.gz | 295.3 KB | Display | PDB format |
PDBx/mmJSON format | 7dq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/7dq6 ftp://data.pdbj.org/pub/pdb/validation_reports/dq/7dq6 | HTTPS FTP |
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-Related structure data
Related structure data | 7dq5SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 9 - 528 / Label seq-ID: 25 - 544
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-Components
#1: Protein | Mass: 59674.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Embleya scabrispora (bacteria) / Gene: hitB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7R6G7 #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: 2.29 Å3/Da / Density % sol: 46.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 400, calcium acetate, sodium acetate |
-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: Dec 10, 2019 |
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: 2.6→50 Å / Num. obs: 34560 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4167 / CC1/2: 0.861 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DQ5 Resolution: 2.6→48.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.905 / SU B: 32.333 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.734 / ESU R Free: 0.333 / 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: 125.7 Å2 / Biso mean: 63.691 Å2 / Biso min: 28 Å2
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Refinement step | Cycle: final / Resolution: 2.6→48.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 13129 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.6→2.668 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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