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Yorodumi- PDB-4ume: Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ume | ||||||
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Title | Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis in complex with Magnesium ion and KDO molecule | ||||||
Components | 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC | ||||||
Keywords | HYDROLASE / HAD SUPERFAMILY | ||||||
Function / homology | Function and homology information 3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | MORAXELLA CATARRHALIS BC8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Dhindwal, S. / Tomar, S. / Kumar, P. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Ligand-Bound Structures of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase from Moraxella Catarrhalis Reveal a Water Channel Connecting to the Active Site for the Second Step of Catalysis Authors: Dhindwal, S. / Priyadarshini, P. / Patil, D.N. / Tapas, S. / Kumar, P. / Tomar, S. / Kumar, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ume.cif.gz | 50 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ume.ent.gz | 34.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ume.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ume_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 4ume_full_validation.pdf.gz | 447.6 KB | Display | |
Data in XML | 4ume_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 4ume_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/4ume ftp://data.pdbj.org/pub/pdb/validation_reports/um/4ume | HTTPS FTP |
-Related structure data
Related structure data | 4um5C 4um7C 4umdC 4umfC 3n1uS 4um6 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21084.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MORAXELLA CATARRHALIS BC8 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: F1X4B5, UniProt: A0A0J9X241*PLUS, 3-deoxy-manno-octulosonate-8-phosphatase | ||
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#2: Sugar | ChemComp-KDO / | ||
#3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.45 % / Description: NONE |
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Crystal grow | pH: 7 Details: 100 MM MG FORMATE, 100 MM BIS-TRIS PROPANE (PH 5.0), 28% W/V PEG 3350, KDO, NA PHOSPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 10, 2013 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→43.31 Å / Num. obs: 9166 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.07→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4 / % possible all: 77.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N1U Resolution: 2.09→37.38 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.879 / SU B: 6.014 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.223 / 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: 19.361 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→37.38 Å
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Refine LS restraints |
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