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Yorodumi- PDB-7cz2: The complex structure of MSMEG_1954-ADP from Mycobacterium smegmatis -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cz2 | ||||||
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Title | The complex structure of MSMEG_1954-ADP 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 / Protein kinase-like domain superfamily / ADENOSINE-5'-DIPHOSPHATE / ABC1 family protein Function and homology information | ||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 | 7cz2.cif.gz | 89.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cz2.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 7cz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/7cz2 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/7cz2 | HTTPS FTP |
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-Related structure data
Related structure data | 7cy2C 7cyrC 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 on special symmetry positions |
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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-ADP / | ||||||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | 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: 2.12 Å3/Da / Density % sol: 42.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M calcium acetate hydrate, 0.1M sodium cacodylate trihydrate (pH6.5), 18% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 24, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 38277 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.023 / Rrim(I) all: 0.072 / Χ2: 0.979 / Net I/σ(I): 7.8 / Num. measured all: 377947 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.8→38.66 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.709 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 108.01 Å2 / Biso mean: 27.533 Å2 / Biso min: 4.38 Å2
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Refinement step | Cycle: final / Resolution: 1.8→38.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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