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- PDB-2ouw: Crystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ouw | ||||||
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Title | Crystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum rubrum ATCC 11170 at 1.95 A resolution | ||||||
![]() | Alkylhydroperoxidase AhpD core | ||||||
![]() | OXIDOREDUCTASE / YP_425393.1 / Carboxymuconolactone decarboxylase family / Alkylhydroperoxidase AhpD core / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of Alkylhydroperoxidase AhpD core (YP_425393.1) from Rhodospirillum rubrum ATCC 11170 at 1.95 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. | ||||||
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 | ![]() | 66.7 KB | Display | ![]() |
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PDB format | ![]() | 52.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.6 KB | Display | ![]() |
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Full document | ![]() | 456 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 18.5 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 0 - 134 / Label seq-ID: 1 - 135
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF THE HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
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Components
#1: Protein | Mass: 15031.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NA / | #3: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #4: Chemical | ChemComp-ACY / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.8 % |
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Crystal grow | Temperature: 277 K / pH: 4.6 Details: NANODROP, 0.2M (NH4)2SO4, 25.0% PEG 4000, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.60 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2006 / 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: 1.95→48.507 Å / Num. obs: 19429 / % possible obs: 98.8 % / Redundancy: 5.65 % / Biso Wilson estimate: 32.46 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.05 | |||||||||
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 5.69 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2.9 / % possible all: 96.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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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 RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ACETATE (ACY) MOLECULES FROM THE CRYSTALLIZATION WERE MODELED INTO THE STRUCTURE. A SODIUM ION WAS MODELED AT A SPECIAL POSITION BETWEEN TWO SYMMETRY- RELATED ASPARTIC ACID SIDECHAINS. 5. ELECTRON DENSITY INDICATES THE PRESENCE OF AN INTRA-SUBUNIT DISULFIDE BOND BETWEEN THE SIDECHAINS OF CYS 83 AND CYS 86 OF BOTH SUBUNITS IN THE ASYMMETRIC UNIT. 6. THE REFINED CRYSTAL STRUCTURE INDICATES THE SIDECHAIN OF GLU A130 IS SITUATED NEAR A CRYSTALLOGRAPHIC SYMMETRY AXIS, HOWEVER THE POSITIONS OF THE ATOMS FOR THIS RESIDUE ON SUBUNIT A COULD NOT BE RELIABLY MODELED. 7. UNKNOWN LIGANDS (UNL) WERE MODELED INTO THE PUTATIVE ACTIVE SITES ON BOTH SUBUNITS IN THE ASYMMETRIC UNIT.
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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: 38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.507 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1880 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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