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Yorodumi- PDB-6w7s: Ketoreductase from module 1 of the 6-deoxyerythronolide B synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w7s | ||||||
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Title | Ketoreductase from module 1 of the 6-deoxyerythronolide B synthase (KR1) in complex with antibody fragment (Fab) 2G10 | ||||||
Components |
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Keywords | OXIDOREDUCTASE/IMMUNE SYSTEM / ketoreductase / antibody fragment / OXIDOREDUCTASE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information 6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process Similarity search - Function | ||||||
Biological species | Saccharopolyspora erythraea (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Cogan, D.P. / Mathews, I.I. / Khosla, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2020 Title: Antibody Probes of Module 1 of the 6-Deoxyerythronolide B Synthase Reveal an Extended Conformation During Ketoreduction. Authors: Cogan, D.P. / Li, X. / Sevillano, N. / Mathews, I.I. / Matsui, T. / Craik, C.S. / Khosla, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w7s.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w7s.ent.gz | 148.1 KB | Display | PDB format |
PDBx/mmJSON format | 6w7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w7s ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w7s | HTTPS FTP |
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-Related structure data
Related structure data | 6wh9C 2fr0S 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50888.957 Da / Num. of mol.: 1 / Fragment: module 1 (UNP residues 1448-1928) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAI / Plasmid: pAYC59 / Production host: Escherichia coli (E. coli) / Strain (production host): BAP1 / References: UniProt: Q5UNP6, UniProt: Q03131*PLUS |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 27107.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#3: Antibody | Mass: 25305.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) |
-Non-polymers , 3 types, 421 molecules
#4: Chemical | ChemComp-MES / |
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#5: Chemical | ChemComp-CL / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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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: 2.67 Å3/Da / Density % sol: 53.91 % |
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Crystal grow | Temperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 15% PEG6000, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2019 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.249→39.36 Å / Num. obs: 51949 / % possible obs: 99.9 % / Redundancy: 13.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.075 / Rrim(I) all: 0.281 / Net I/σ(I): 8.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2FR0 Resolution: 2.25→39.36 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.08 Å2 / Biso mean: 36.4821 Å2 / Biso min: 13.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→39.36 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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