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Yorodumi- PDB-4bgb: Nucleotide-bound closed form of a putative sugar kinase MK0840 fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bgb | ||||||
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Title | Nucleotide-bound closed form of a putative sugar kinase MK0840 from Methanopyrus kandleri | ||||||
Components | PUTATIVE SUGAR KINASE MK0840 | ||||||
Keywords | TRANSFERASE / PHOSPHOTRANSFER / PSEUDOMUREIN | ||||||
Function / homology | Function and homology information amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / metallopeptidase activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | METHANOPYRUS KANDLERI (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Schacherl, M. / Baumann, U. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structural Characterization of the Ribonuclease H-Like Type Askha Superfamily Kinase Mk0840 from Methanopyrus Kandleri Authors: Schacherl, M. / Waltersperger, S.M. / Baumann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bgb.cif.gz | 284.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bgb.ent.gz | 227.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bgb_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4bgb_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4bgb_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 4bgb_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bgb ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bgb | HTTPS FTP |
-Related structure data
Related structure data | 4bg8C 4bg9C 4bgaSC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35059.656 Da / Num. of mol.: 2 / Fragment: RESIDUES 37-358 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOPYRUS KANDLERI (archaea) / Strain: AV19 / Description: DSM6324 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TX37 |
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-Non-polymers , 6 types, 537 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-K / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | GLYCEROL (GOL): GOL7 ONLY PARTIALLY OCCUPIED |
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Sequence details | TRUNCATED CONSTRUCT LACKING THE FIRST 36 AMINO ACIDS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % Description: PARTIAL MODEL SOLVED BY MR. MODEL FOR SECOND PROTOMER - CLOSED FORM - BUILD BY WEB-BASED ARPWARP. MERGED DATASET FROM LOW-RESOLUTION AND HIGH-RESOLUTION PASS. |
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Crystal grow | pH: 4.6 Details: 0.14 M CACL2, 0.07 M SODIUM ACETATE PH 4.6, 10 % ISOPROPANOL AND 28% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 8, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→45.2 Å / Num. obs: 154630 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.12 |
Reflection shell | Resolution: 1.34→1.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.61 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BGA CHAIN A Resolution: 1.34→45.147 Å / SU ML: 0.13 / σ(F): 1.99 / Phase error: 20.02 / Stereochemistry target values: ML Details: FIRST 36 AMINO ACIDS OF THE PROTEIN ARE MISSING. GSH OVERHANG FROM THROMBIN-DIGESTED 6X-HIS TAG.
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.413 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→45.147 Å
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Refine LS restraints |
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LS refinement shell |
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