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Yorodumi- PDB-2hx5: Crystal structure of a putative thioesterase (pmt_2055) from proc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hx5 | ||||||
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Title | Crystal structure of a putative thioesterase (pmt_2055) from prochlorococcus marinus str. mit 9313 at 1.50 A resolution | ||||||
Components | Hypothetical protein | ||||||
Keywords | HYDROLASE / Thioesterase/thiol ester dehydrase-isomerase fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information 1,4-dihydroxy-2-naphthoyl-CoA hydrolase / phylloquinone biosynthetic process / thiolester hydrolase activity Similarity search - Function | ||||||
Biological species | Prochlorococcus marinus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of hypothetical protein (NP_895880.1) from Prochlorococcus marinus MIT9313 at 1.50 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 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A TETRAMER 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 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hx5.cif.gz | 45.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hx5.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hx5_validation.pdf.gz | 432 KB | Display | wwPDB validaton report |
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Full document | 2hx5_full_validation.pdf.gz | 433.4 KB | Display | |
Data in XML | 2hx5_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 2hx5_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/2hx5 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/2hx5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE |
-Components
#1: Protein | Mass: 17526.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prochlorococcus marinus (bacteria) / Strain: MIT 9313 / Gene: NP_895880.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7V4A7 | ||
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#2: Chemical | #3: 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: 2.44 Å3/Da / Density % sol: 49.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5 Details: 35.0% 2-ethoxyethanol, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 17, 2006 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→27.853 Å / Num. obs: 30132 / % possible obs: 95.3 % / Biso Wilson estimate: 25.327 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.55 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→27.853 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.317 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.061 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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3) THERE IS UNKNOWN DENSITY NEAR GLU104. THIS WAS LEFT UNMODELED. THE UNKNOWN DENSITY IS LOCATED NEAR THE ACTIVE SITE OF THE PROTEIN. THIS COULD BE PART OF COA. (4). 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.349 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→27.853 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 40.3951 Å / Origin y: 46.5673 Å / Origin z: 11.0461 Å
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Refinement TLS group | Selection: ALL |