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Yorodumi- PDB-2hbo: Crystal structure of a thioesterase superfamily protein (cc_3309)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hbo | ||||||
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Title | Crystal structure of a thioesterase superfamily protein (cc_3309) from caulobacter vibrioides at 1.85 A resolution | ||||||
Components | Hypothetical protein (np_422103.1)Hypothesis | ||||||
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 | ||||||
Biological species | Caulobacter vibrioides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of hypothetical protein (np_422103.1) from Caulobacter crescentus at 1.85 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hbo.cif.gz | 42 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hbo.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 2hbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/2hbo ftp://data.pdbj.org/pub/pdb/validation_reports/hb/2hbo | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 17780.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: np_422103.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A395 | ||
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#2: Chemical | ChemComp-PE4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal |
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Crystal grow |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.85→50 Å / Num. obs: 12896 / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.073 / Χ2: 0.973 / Net I/σ(I): 13.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.85→28.1 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.068 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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. PEG-3350 HAS BEEN PARTIALLED MODELED AS PE4. 4. THERE ARE SOME POSITIVE DIFFERENCE DENSITIES AROUND PEG THAT SUGGEST THAT PEG MOLECULE MIGHT OCCUPY ALTERNATE CONFORMATIONS WITH PARTIAL OCCUPANCIES. 5. ETHYLENE GLYCOL (EDO) FROM CRYO CONDITION HAS BEEN MODELED. 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: 36.857 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→28.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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