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- PDB-2hhz: Crystal structure of a pyridoxamine 5'-phosphate oxidase-related ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2hhz | ||||||
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Title | Crystal structure of a pyridoxamine 5'-phosphate oxidase-related protein (ssuidraft_2804) from streptococcus suis 89/1591 at 2.00 A resolution | ||||||
![]() | Pyridoxamine 5'-phosphate oxidase-related | ||||||
![]() | OXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / Roll / Mainly Beta / ACETATE ION / PHOSPHATE ION / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Pyridoxamine 5'-phosphate oxidase-related (ZP_00875725.1) from STREPTOCOCCUS SUIS 89-1591 at 2.00 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.1 KB | Display | ![]() |
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PDB format | ![]() | 31 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.4 KB | Display | ![]() |
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Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17485.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q2ZZ07, pyridoxal 5'-phosphate synthase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5 Details: 40.0% PEG-400, 0.1M Acetate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2006 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→29.198 Å / Num. obs: 10580 / % possible obs: 94.4 % / Biso Wilson estimate: 40.243 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.48 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. RESIDUES 107-111 AND 140-144 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. CL, ACT, PO4 MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. THERE ARE UNMODELED DENSITY NEAR RESIDUES A122 AND A133. 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.918 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.198 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.2351 Å / Origin y: 35.9856 Å / Origin z: 25.6993 Å
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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