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- PDB-3ch0: Crystal structure of glycerophosphoryl diester phosphodiesterase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ch0 | ||||||
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Title | Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution | ||||||
![]() | Glycerophosphodiester phosphodiesterase | ||||||
![]() | HYDROLASE / YP_677622.1 / glycerophosphoryl diester phosphodiesterase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | ![]() glycerophosphodiester phosphodiesterase / glycerophosphodiester phosphodiesterase activity / lipid metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of glycerophosphoryl diester phosphodiesterase (YP_677622.1) from Cytophaga hutchinsonii ATCC 33406 at 1.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.8 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.2 KB | Display | ![]() |
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Full document | ![]() | 466.7 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
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Components
#1: Protein | Mass: 31104.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Cytophaga hutchinsonii / Strain: NCIMB 9469 / Gene: YP_677622.1, ugpQ, CHU_1005 / Plasmid: SpeedET / Production host: ![]() ![]() References: UniProt: Q11WD4, UniProt: A0A6N4SPL7*PLUS, glycerophosphodiester phosphodiesterase | ||||||
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#2: Chemical | ChemComp-CIT / | ||||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: NANODROP, 14.0% PEG 4000, 24.227% 2-propanol, 5.0% Glycerol, 0.1M Citric acid pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2008 / Details: Flat mirror (vertical focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→29.553 Å / Num. obs: 56237 / % possible obs: 100 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.783 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 6.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. CITRATE (CIT) AND GLYCEROL (GOL) MOLECULES FROM CRYSTALLIZATION AND ETHYLENE GLYCOL (EDO) FROM CRYO SOLUTION WERE MODELED.
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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: 13.008 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.553 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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