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- PDB-4umf: Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate pho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4umf | ||||||
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Title | Crystal structure of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis in complex with Magnesium ion, Phosphate ion and KDO molecule | ||||||
![]() | 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE PHOSPHATASE KDSC | ||||||
![]() | HYDROLASE / HAD SUPERFAMILY | ||||||
Function / homology | ![]() 3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dhindwal, S. / Tomar, S. / Kumar, P. | ||||||
![]() | ![]() 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 283.7 KB | Display | ![]() |
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PDB format | ![]() | 232.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4um5C ![]() 4um7C ![]() 4umdC ![]() 4umeC ![]() 3n1uS ![]() 4um6 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21084.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: F1X4B5, UniProt: A0A0J9X241*PLUS, 3-deoxy-manno-octulosonate-8-phosphatase #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-MG / #4: Sugar | ChemComp-KDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.8 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 100 MM MG FORMATE, 100 MM BIS-TRIS PROPANE (PH 5.0), 28% W/V PEG 3350, 200MM SODIUM PHOSPHATE, KDO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR / Detector: IMAGE PLATE / Date: Feb 27, 2014 / 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: 2.28→50 Å / Num. obs: 33990 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.28→2.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.01 / % possible all: 65 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3N1U Resolution: 2.28→31.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.314 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.513 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES WITH TLS ADDED
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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: 65.493 Å2
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Refinement step | Cycle: LAST / Resolution: 2.28→31.69 Å
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Refine LS restraints |
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