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Yorodumi- PDB-3k2k: Crystal structure of putative carboxypeptidase (YP_103406.1) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k2k | ||||||
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Title | Crystal structure of putative carboxypeptidase (YP_103406.1) from BURKHOLDERIA MALLEI ATCC 23344 at 2.49 A resolution | ||||||
Components | putative carboxypeptidase | ||||||
Keywords | HYDROLASE / putative carboxypeptidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia mallei ATCC 23344 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative carboxypeptidase (YP_103406.1) from BURKHOLDERIA MALLEI ATCC 23344 at 2.49 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k2k.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k2k.ent.gz | 72.5 KB | Display | PDB format |
PDBx/mmJSON format | 3k2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k2k_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 3k2k_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 3k2k_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 3k2k_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/3k2k ftp://data.pdbj.org/pub/pdb/validation_reports/k2/3k2k | 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 | CRYSTAL PACKING ANALYSIS AND SIZE EXCLUSION CHROMATOGRAPHY COMBINED WITH STATIC LIGHT SCATTERING SUGGEST THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION UNDER THE CONDITIONS TESTED. |
-Components
#1: Protein | Mass: 46063.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia mallei ATCC 23344 (bacteria) Gene: BMA1798 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q62IR3, UniProt: A0A0H2WJQ2*PLUS | ||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.31 Å3/Da |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 4.3000M NaCl, 0.1M HEPES pH 7.5, Additive: 0.006 M calcium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97931 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 7, 2009 Details: Flat mirror, vertical and horizontal focussing mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.49→29.553 Å / Num. obs: 34624 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 61.88 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.45 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 2.49→29.553 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.767 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.148 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.CHLORIDE (CL) AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION AND CRYOPROTECTION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.THE RAMACHANDRAN OUTLIER AT GLN39 IS SUPPORTED BY ELECTRON 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.38 Å2 / Biso mean: 36.226 Å2 / Biso min: 12.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→29.553 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.492→2.557 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 107.7147 Å / Origin y: 2.1292 Å / Origin z: 33.0333 Å
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