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Yorodumi- PDB-3b9t: Crystal structure of predicted acetamidase/formamidase (YP_546212... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b9t | ||||||
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Title | Crystal structure of predicted acetamidase/formamidase (YP_546212.1) from Methylobacillus flagellatus KT at 1.58 A resolution | ||||||
Components | Twin-arginine translocation pathway signal protein | ||||||
Keywords | HYDROLASE / YP_546212.1 / predicted acetamidase/formamidase / Acetamidase/Formamidase family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Acetamidase/Formamidase / Acetamidase/Formamidase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding / Twin-arginine translocation pathway signal Function and homology information | ||||||
Biological species | Methylobacillus flagellatus KT (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of predicted acetamidase/formamidase (YP_546212.1) from Methylobacillus flagellatus KT at 1.58 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. 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. 2. A PUTATIVE TWIN ARGININE SIGNAL PEPTIDE CLEAVAGE SITE IS LOCATED BETWEEN RESIDUES 57 AND 58. MASS SPECTROMETRY INDICATED THAT THE FULL LENGTH PROTEIN WAS PRESENT DURING PURIFICATION, HOWEVER, IT IS POSSIBLE THAT THE SHORTER CLEAVED PRODUCT WAS CRYSTALLIZED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b9t.cif.gz | 380.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b9t.ent.gz | 308.6 KB | Display | PDB format |
PDBx/mmJSON format | 3b9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b9t_validation.pdf.gz | 481.9 KB | Display | wwPDB validaton report |
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Full document | 3b9t_full_validation.pdf.gz | 487.6 KB | Display | |
Data in XML | 3b9t_validation.xml.gz | 73.7 KB | Display | |
Data in CIF | 3b9t_validation.cif.gz | 114.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9t ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9t | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: HIS / End label comp-ID: GLY / Refine code: 5 / Auth seq-ID: 69 - 480 / Label seq-ID: 70 - 481
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 53558.922 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria) Species: Methylobacillus flagellatus / Strain: KT, DSM 6875 / Gene: YP_546212.1, Mfla_2104 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GZG6 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Sequence details | REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: NANODROP, 1.0M LiCl, 20.0% PEG 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9796 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007 / Details: KOHZU: Double crystal Si(111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.58→29.814 Å / Num. obs: 196551 / % possible obs: 95.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 13.67 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.58→29.814 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.099 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.082 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. EDO, CL MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. MG IONS ARE MODELED BASED ON DENSITY AND COORDINATION. THE ASSIGNMENT OF MG AND THE EDO NEXT TO IT IS TENTATIVE. 6. THERE ARE NO DENSITIES FOR THE N-TERMINAL RESIDUES 0-63 OF A/C/D CHAINS AND 0-67 OF B CHAIN ALTHOUGH MASS SPECTROSCOPY INDICATED THAT THEY ARE LIKELY TO BE PRESENT DURING PURIFICATION. THE SEQUENCE ANALYSIS INDICATED THAT THIS PROTEIN LIKELY CONTAINS A TWIN ARGININE SIGNAL PEPTIDE WITH A PUTATIVE CLEAVAGE SITE BETWEEN RESIDUES 57 AND 58. AS A RESULT, IT IS ALSO POSSIBLE THAT THE SHORTER CLEAVED PRODUCT WAS CRYSTALLIZED. 7. RAMACHANDRAN OUTLIERS 349 FOR ALL CHAINS ARE SUPPORTED BY WELL DEFINED DENSITY.
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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: 13.157 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→29.814 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.58→1.621 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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