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Yorodumi- PDB-4f72: Crystal structure of had family enzyme bt-2542 (target efi-501088... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f72 | ||||||
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Title | Crystal structure of had family enzyme bt-2542 (target efi-501088) from Bacteroides thetaiotaomicron, asp12ala mutant, complex with magnesium and inorganic phosphate | ||||||
Components | Putative haloacid dehalogenase-like hydrolase | ||||||
Keywords | HYDROLASE / MAGNESIUM BINDING SITE / ENZYME FUNCTION INITIATIVE / Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Patskovsky, Y. / Farelli, J.D. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Patskovsky, Y. / Farelli, J.D. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Imker, H.J. / Zencheck, W.D. / Gerlt, J.A. / Allen, K.N. / Dunaway-Mariano, D. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Protein Bt-2542 from Bacteroides Thetaiotaomicron (Target Efi-501088) Authors: Patskovsky, Y. / Farelli, J.D. / Toro, R. / Bhosle, R. / Hillerich, B. / Washington, E. / Seidel, R.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, ...Authors: Patskovsky, Y. / Farelli, J.D. / Toro, R. / Bhosle, R. / Hillerich, B. / Washington, E. / Seidel, R.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Allen, K.N. / Dunaway-Mariano, D. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f72.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f72.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 4f72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/4f72 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/4f72 | HTTPS FTP |
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-Related structure data
Related structure data | 4dfdC 4f71C 4dccS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26777.783 Da / Num. of mol.: 2 / Mutation: D12A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2542 / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A4Q5 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 0.2M MAGNESIUM FORMATE, PH 5.9, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→70 Å / Num. obs: 20508 / % possible obs: 99.1 % / Observed criterion σ(I): -5 / Redundancy: 6.9 % / Biso Wilson estimate: 62.951 Å2 / Rsym value: 0.087 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.7 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement Starting model: 4DCC Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / SU B: 10.838 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 0.398 / ESU R Free: 0.299 / 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 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.623 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.403→2.465 Å / Total num. of bins used: 20
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