+Open data
-Basic information
Entry | Database: PDB / ID: 6lfa | ||||||
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Title | Structure of the N-terminal domain of Wag31 | ||||||
Components | Cell wall synthesis protein Wag31 | ||||||
Keywords | LIPID BINDING PROTEIN / DivIVA / Wag31 / Mycobacterial polar growth | ||||||
Function / homology | Function and homology information peptidoglycan-based cell wall biogenesis / regulation of growth rate / cell pole / peptidoglycan-based cell wall / regulation of cell shape / protein stabilization / cell cycle / cell division / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chaudhuri, B.N. / Choukate, K. | ||||||
Citation | Journal: Iucrj / Year: 2020 Title: Structural basis of self-assembly in the lipid-binding domain of mycobacterial polar growth factor Wag31 Authors: Chaudhuri, B.N. / Choukate, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lfa.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lfa.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 6lfa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/6lfa ftp://data.pdbj.org/pub/pdb/validation_reports/lf/6lfa | HTTPS FTP |
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-Related structure data
Related structure data | 2wujS S: Starting model for refinement |
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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: 8667.498 Da / Num. of mol.: 2 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: wag31, ag84, Rv2145c, MTCY270.23 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMU1 #2: Chemical | ChemComp-PGE / | #3: Water | ChemComp-HOH / | 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: 2.18 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 6.5 Details: 0.2 M MgCl2, 0.1 M Na cacodylate, 50% (v/v) PEG 200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30.08 Å / Num. obs: 6374 / % possible obs: 98.56 % / Redundancy: 12.1 % / Biso Wilson estimate: 21.75 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.07 / Rrim(I) all: 0.245 / Net I/σ(I): 7.45 |
Reflection shell | Resolution: 2.301→2.383 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 592 / CC1/2: 0.765 / Rpim(I) all: 0.345 / % possible all: 92.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WUJ Resolution: 2.3→30.08 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 32.58 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30.08 Å
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Refine LS restraints | Type: f_dihedral_angle_d / Dev ideal: 12.8239 / Number: 688 | ||||||||||||||||||||
LS refinement shell | Resolution: 2.301→2.383 Å
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