+Open data
-Basic information
Entry | Database: PDB / ID: 3guu | ||||||
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Title | X-ray structure of Candida Antarctica lipase A | ||||||
Components | Lipase A | ||||||
Keywords | HYDROLASE / Candida / Lipase / Protein structure | ||||||
Function / homology | Function and homology information triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Candida Antarctica (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Brandt, A.-M. / Li, X.-G. / Nymalm-Rejstrom, Y. / Airenne, T. / Kanerva, L.T. / Salminen, T.A. | ||||||
Citation | Journal: To be Published Title: The crystal structure of Lipase A from Candida antarctica Authors: Brandt, A.-M. / Li, X.-G. / Nymalm-Rejstrom, Y. / Airenne, T. / Kanerva, L.T. / Salminen, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3guu.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3guu.ent.gz | 145.1 KB | Display | PDB format |
PDBx/mmJSON format | 3guu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/3guu ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3guu | HTTPS FTP |
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-Related structure data
Related structure data | 2veoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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 auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 12 - 441 / Label seq-ID: 33 - 462
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-Components
#1: Protein | Mass: 49345.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Commerial enzyme Roche Chirazyme L-5 / Source: (natural) Candida Antarctica (fungus) / References: UniProt: W3VKA4*PLUS, triacylglycerol lipase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | Sequence details | THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THIS ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING | |
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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: 3.23 Å3/Da / Density % sol: 61.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.5M Ammonium sulfate, 12% glycerol, 100mM TRIS-HCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 294.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 88351 / Num. obs: 86764 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 9.64 |
Reflection shell | Resolution: 2.1→2.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 4.42 / Num. unique all: 17290 / Rsym value: 0.434 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VEO Resolution: 2.1→19.92 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 4.309 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 14.292 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.92 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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