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Yorodumi- PDB-3hoa: Crystal structure of the Thermus thermophilus M32 carboxypeptidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hoa | ||||||
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Title | Crystal structure of the Thermus thermophilus M32 carboxypeptidase | ||||||
Components | Thermostable carboxypeptidase 1 | ||||||
Keywords | HYDROLASE / proline-rich loop / Carboxypeptidase | ||||||
Function / homology | Function and homology information carboxypeptidase Taq / metallocarboxypeptidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lee, M.M. / Chan, M.K. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: Insight into the substrate length restriction of M32 carboxypeptidases: Characterization of two distinct subfamilies. Authors: Lee, M.M. / Isaza, C.E. / White, J.D. / Chen, R.P. / Liang, G.F. / He, H.T. / Chan, S.I. / Chan, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hoa.cif.gz | 216.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hoa.ent.gz | 173.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hoa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hoa_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 3hoa_full_validation.pdf.gz | 452.7 KB | Display | |
Data in XML | 3hoa_validation.xml.gz | 42 KB | Display | |
Data in CIF | 3hoa_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/3hoa ftp://data.pdbj.org/pub/pdb/validation_reports/ho/3hoa | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 58031.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / DSM 7039 / Gene: TT_C1715 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q72GY3, carboxypeptidase Taq #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 0.1 M Na-citrate pH 4.0, 8% w/v PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.00002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2003 Details: 1m long Rh coated bent cylindrical mirror for horizontal and vertical focusing |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→45.7 Å / Num. all: 60029 / Num. obs: 60029 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.417 % / Biso Wilson estimate: 2.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.1→2.23 Å / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 5.1 / Num. unique all: 8712 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Bacillus subtilis carboxypeptidase Resolution: 2.1→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 132243.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7339 Å2 / ksol: 0.380191 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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