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Yorodumi- PDB-7kem: Crystallographic structure of L,D-transpeptidase 2 from Mycobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kem | ||||||
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Title | Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis | ||||||
Components | L,D-transpeptidase 2 | ||||||
Keywords | TRANSFERASE / Transpeptidase / Peptidoglycan synthesis | ||||||
Function / homology | Function and homology information peptidoglycan-protein cross-linking / peptidoglycan L,D-transpeptidase activity / Transferases; Acyltransferases; Aminoacyltransferases / acyltransferase activity / cell wall organization / regulation of cell shape / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Libreros, G.A. / Dias, M.V.B. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: To Be Published Title: Crystallographic structure of L,D-transpeptidase 2 from Mycobacterium tuberculosis. Authors: Libreros, G.A. / Dias, M.V.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kem.cif.gz | 120.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kem.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 7kem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kem_validation.pdf.gz | 519.5 KB | Display | wwPDB validaton report |
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Full document | 7kem_full_validation.pdf.gz | 526.5 KB | Display | |
Data in XML | 7kem_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 7kem_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/7kem ftp://data.pdbj.org/pub/pdb/validation_reports/ke/7kem | HTTPS FTP |
-Related structure data
Related structure data | 3turS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43407.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: ldtB, lppS, Rv2518c, RVBD_2518c, P425_02624 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: I6Y9J2, Transferases; Acyltransferases; Aminoacyltransferases #2: Chemical | ChemComp-0JC / #3: Chemical | ChemComp-DGL / | #4: Chemical | ChemComp-6CL / | #5: Chemical | ChemComp-PT / | 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: 2.51 Å3/Da / Density % sol: 51.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 3M NaOAc |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.458 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→49.66 Å / Num. obs: 80670 / % possible obs: 99.6 % / Redundancy: 12.3 % / Biso Wilson estimate: 22.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.108 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8453 / CC1/2: 0.824 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TUR Resolution: 1.77→49.66 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.914 / SU B: 2.876 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 94.58 Å2 / Biso mean: 25.543 Å2 / Biso min: 13.35 Å2
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Refinement step | Cycle: final / Resolution: 1.77→49.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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