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- PDB-7c1s: Crystal structure of the starter condensation domain of rhizomide... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c1s | ||||||
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Title | Crystal structure of the starter condensation domain of rhizomide synthetase RzmA mutant H140A/R148A in complex with C8-CoA and Leu-SNAC | ||||||
![]() | Non-ribosomal peptide synthetase modules | ||||||
![]() | BIOSYNTHETIC PROTEIN / nonribosomal peptide synthesis / RzmA-Cs / starter condensation (Cs) domains / C8-CoA / Leu-SNAC | ||||||
Function / homology | ![]() Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / : / amino acid activation for nonribosomal peptide biosynthetic process / carboxylic acid metabolic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhong, L. / Diao, X. / Zhang, N. / Li, F.W. / Zhou, H.B. / Chen, H.N. / Ren, X. / Zhang, Y. / Wu, D. / Bian, X. | ||||||
![]() | ![]() Title: Engineering and elucidation of the lipoinitiation process in nonribosomal peptide biosynthesis. Authors: Zhong, L. / Diao, X. / Zhang, N. / Li, F. / Zhou, H. / Chen, H. / Bai, X. / Ren, X. / Zhang, Y. / Wu, D. / Bian, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.9 KB | Display | ![]() |
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PDB format | ![]() | 150.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 883.2 KB | Display | ![]() |
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Full document | ![]() | 888.5 KB | Display | |
Data in XML | ![]() | 18.5 KB | Display | |
Data in CIF | ![]() | 25.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c1hSC ![]() 7c1kC ![]() 7c1lC ![]() 7c1pC ![]() 7c1rC ![]() 7c1uC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48418.785 Da / Num. of mol.: 1 / Mutation: H140V, R148A Source method: isolated from a genetically manipulated source Details: rhizomide synthetase RzmA Source: (gene. exp.) ![]() Strain: HKI 454 / Gene: RBRH_01504 / Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: E5ATN9, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Chemical | ChemComp-CO8 / |
#3: Chemical | ChemComp-FGU / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.63 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: BIS-TRIS propane, PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 31, 2019 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.58→50 Å / Num. obs: 13590 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.044 / Rrim(I) all: 0.158 / Χ2: 0.985 / Net I/σ(I): 4.6 / Num. measured all: 172673 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7C1H Resolution: 2.586→30.115 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.45 / 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: 126.31 Å2 / Biso mean: 46.0472 Å2 / Biso min: 18.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.586→30.115 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 12.0923 Å / Origin y: 21.923 Å / Origin z: 25.2402 Å
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Refinement TLS group |
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