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Yorodumi- PDB-1zmb: Crystal Structure of the Putative Acetylxylan Esterase from Clost... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zmb | ||||||
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Title | Crystal Structure of the Putative Acetylxylan Esterase from Clostridium acetobutylicum, Northeast Structural Genomics Target CaR6 | ||||||
Components | Acetylxylan esterase related enzyme | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å | ||||||
Authors | Forouhar, F. / Vorobiev, S.M. / Abashidze, M. / Ciao, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Putative Acetylxylan Esterase from Clostridium acetobutylicum, Northeast Structural Genomics Target CaR6 Authors: Forouhar, F. / Vorobiev, S.M. / Abashidze, M. / Ciao, M. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zmb.cif.gz | 334 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zmb.ent.gz | 287.8 KB | Display | PDB format |
PDBx/mmJSON format | 1zmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zmb_validation.pdf.gz | 481.9 KB | Display | wwPDB validaton report |
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Full document | 1zmb_full_validation.pdf.gz | 535.6 KB | Display | |
Data in XML | 1zmb_validation.xml.gz | 64.1 KB | Display | |
Data in CIF | 1zmb_validation.cif.gz | 86.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/1zmb ftp://data.pdbj.org/pub/pdb/validation_reports/zm/1zmb | 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 33720.801 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Plasmid: pET21(BL21) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q97LM8 #2: 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: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM MES, 10% PEG 20K, and 5 mM DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2005 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 124903 / Num. obs: 118658 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.076 / Net I/σ(I): 14.04 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3 / Num. unique all: 11527 / Rsym value: 0.341 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.61→29.31 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 243470.2 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 13.2867 Å2 / ksol: 0.316861 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 35 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.61→29.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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