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Yorodumi- PDB-5bpf: Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bpf | ||||||
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Title | Crystal structure of ADP complexed D-alanine-D-alanine ligase(DDL) from Yersinia pestis | ||||||
Components | D-alanine-D-alanine ligase | ||||||
Keywords | LIGASE / D-alanine-D-alanine ligase (DDL) / drug target / bacterial cell wall synthesis / Yersinia pestis | ||||||
Function / homology | Function and homology information D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Tran, H.T. / Kang, L.W. / Hong, M.K. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop. Authors: Tran, H.T. / Hong, M.K. / Ngo, H.P. / Huynh, K.H. / Ahn, Y.J. / Wang, Z. / Kang, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bpf.cif.gz | 248.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bpf.ent.gz | 198.7 KB | Display | PDB format |
PDBx/mmJSON format | 5bpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bpf_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5bpf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5bpf_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 5bpf_validation.cif.gz | 67.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/5bpf ftp://data.pdbj.org/pub/pdb/validation_reports/bp/5bpf | HTTPS FTP |
-Related structure data
Related structure data | 4zqiSC 5bphC 5c1oC 5c1pC C: citing same article (ref.) 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 33179.789 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: ddl, ddlB, YPO0557, y3624, YP_3627 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8ZIE7, D-alanine-D-alanine ligase |
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-Non-polymers , 5 types, 427 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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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: 2.67 Å3/Da / Density % sol: 53.87 % / Description: orthorhombic shaped crystal |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M sodium acetate, 0.1 M Bis-Tris pH 7.0, 29% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9997 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2013 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9997 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 64040 / % possible obs: 99.9 % / Redundancy: 7.21 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 33.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZQI Resolution: 2.28→37.51 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.147 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 37.005 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→37.51 Å
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Refine LS restraints |
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