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Yorodumi- PDB-3msr: The crystal structure of an amidohydrolase from Mycoplasma synoviae -
+Open data
-Basic information
Entry | Database: PDB / ID: 3msr | ||||||
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Title | The crystal structure of an amidohydrolase from Mycoplasma synoviae | ||||||
Components | amidohydrolasesAmidohydrolase | ||||||
Keywords | HYDROLASE / amidohydrolases / HAD / PSI / SGX / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information 5-phospho-D-xylono-1,4-lactonase / 1,4-lactonase / 1,4-lactonase activity / catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Mycoplasma synoviae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.162 Å | ||||||
Authors | Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of an amidohydrolase from Mycoplasma synoviae Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3msr.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3msr.ent.gz | 67.9 KB | Display | PDB format |
PDBx/mmJSON format | 3msr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/3msr ftp://data.pdbj.org/pub/pdb/validation_reports/ms/3msr | 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 41098.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasma synoviae (bacteria) / Strain: 53 / Gene: HAD, MS53_0025 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) Strain (production host): BL21(DE3)+codon+RIL (p)-stratagene References: UniProt: Q4A724 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-PO4 / |
#4: 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: 3.01 Å3/Da / Density % sol: 59.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M Potassium sodium tartrate tetrahydate, 0.1 M Sodium citrate tribasic dihydrate pH5.6, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→50 Å / Num. obs: 27549 / % possible obs: 99.4 % / Redundancy: 29.7 % / Biso Wilson estimate: 15.44 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.16→2.24 Å / Redundancy: 29.5 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2673 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.162→41.587 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.61 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.38 Å2
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Refinement step | Cycle: LAST / Resolution: 2.162→41.587 Å
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Refine LS restraints |
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LS refinement shell |
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