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Yorodumi- PDB-7cyr: The closed conformation of MSMEG_1954 from Mycobacterium smegmatis -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cyr | ||||||
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Title | The closed conformation of MSMEG_1954 from Mycobacterium smegmatis | ||||||
Components | ABC1 family protein | ||||||
Keywords | TRANSPORT PROTEIN / antibiotic binding / ADP binding | ||||||
Function / homology | ABC1 atypical kinase-like domain / ADCK3-like domain / ABC1 atypical kinase-like domain / ubiquinone biosynthetic process / nucleotide binding / Protein kinase-like domain superfamily / metal ion binding / ACETATE ION / ABC1 family protein Function and homology information | ||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Zhang, Q. / Rao, Z.H. | ||||||
Funding support | China, 1items
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Citation | Journal: Front Microbiol / Year: 2021 Title: Conformational Changes in a Macrolide Antibiotic Binding Protein From Mycobacterium smegmatis Upon ADP Binding. Authors: Zhang, Q. / Liu, X. / Liu, H. / Zhang, B. / Yang, H. / Mi, K. / Guddat, L.W. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cyr.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cyr.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 7cyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cyr_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 7cyr_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 7cyr_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 7cyr_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/7cyr ftp://data.pdbj.org/pub/pdb/validation_reports/cy/7cyr | HTTPS FTP |
-Related structure data
Related structure data | 7cy2C 7cz2C 5yjzS 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
#1: Protein | Mass: 47915.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Gene: MSMEG_1954 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0QTT2 |
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#2: Chemical | ChemComp-ACT / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
Sequence details | The protein was expression with following sequence: ...The protein was expression with following sequence: MSPILGYWKI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium acetate, 0.1M Hepes (pH7.5), 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.046→50 Å / Num. obs: 24869 / % possible obs: 99.3 % / Redundancy: 13.3 % / Biso Wilson estimate: 24.46 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.084 / Χ2: 0.986 / Net I/σ(I): 9.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YJZ Resolution: 2.05→40.321 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.88 / 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: 169.77 Å2 / Biso mean: 33.41 Å2 / Biso min: 10.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→40.321 Å
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Refine LS restraints |
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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: -12.4236 Å / Origin y: 10.2192 Å / Origin z: -22.9987 Å
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Refinement TLS group |
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