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Yorodumi- PDB-2w7z: Structure of the pentapeptide repeat protein EfsQnr, a DNA gyrase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w7z | ||||||
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Title | Structure of the pentapeptide repeat protein EfsQnr, a DNA gyrase inhibitor. Free amines modified by cyclic pentylation with glutaraldehyde. | ||||||
Components | PENTAPEPTIDE REPEAT FAMILY PROTEIN | ||||||
Keywords | INHIBITOR / GLUTARALDEHYDE / GYRASE INHIBITOR / CYCLIC PENTYLATION / CHEMICAL MODIFICATION / PENTAPEPTIDE REPEAT PROTEIN | ||||||
Function / homology | Pentapeptide repeats (8 copies) / E3 ubiquitin-protein ligase SopA / Pentapeptide repeats (9 copies) / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / Pentapeptide repeat family protein Function and homology information | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.6 Å | ||||||
Authors | Vetting, M.W. / Hegde, S.S. / Blanchard, J.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Crystallization of a Pentapeptide-Repeat Protein by Reductive Cyclic Pentylation of Free Amines with Glutaraldehyde. Authors: Vetting, M.W. / Hegde, S.S. / Blanchard, J.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w7z.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w7z.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 2w7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w7z_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 2w7z_full_validation.pdf.gz | 432 KB | Display | |
Data in XML | 2w7z_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 2w7z_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/2w7z ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w7z | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8509, -0.5237, -0.04045), Vector: |
-Components
#1: Protein | Mass: 25023.357 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: CHEMICAL MODIFICATION OF THE FREE AMINES (LYSINES, N-TERMINUS) BY TREATMENT WITH GLUTARALDEHYDE UNDER REDUCING CONDITIONS Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q837D8 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Nonpolymer details | LYSYL-PIPERIDINE (LPD): UNSATURATED SIX-MEMBERED RING, WITH PROTONATED NITROGEN, SP3 GEOMETRY, AND ...LYSYL-PIPERIDINE | |
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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 Å3/Da / Density % sol: 38.14 % / Description: NONE |
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Crystal grow | pH: 6 Details: PROTEIN - 10 MG/ML, 400 MM AMMONIUM SULFATE, 15 MM HEPES PH 7.5, 1 MM DTT, 1 MM ETDA PRECIPITANT - 100 MM MES PH 6.5, 5-15% PEG 6000, 1M LICL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS IV / Date: Jan 2, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20.6 Å / Num. obs: 53909 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.6→94.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.462 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROTEIN WAS PRODUCED WITH N-TERMINAL THROMBIN CLEAVABLE TAG. PROTEIN WAS CRYSTALLIZED AFTER THROMBIN CLEAVAGE, LEAVING A NON-NATIVE N-TERMINUS OF GLYSERHIS-MET1
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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: 15.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→94.07 Å
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Refine LS restraints |
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