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Yorodumi- PDB-2yml: Native L-haloacid dehalogenase from a Rhodobacteraceae family bac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yml | ||||||
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Title | Native L-haloacid dehalogenase from a Rhodobacteraceae family bacterium | ||||||
Components | L-HALOACID DEHALOGENASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | RHODOBACTERACEAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Novak, H.R. / Sayer, C. / Isupov, M.N. / Paszkiewicz, K. / Gotz, D. / Spragg, A.M. / Littlechild, J.A. | ||||||
Citation | Journal: FEBS J. / Year: 2013 Title: Marine Rhodobacteraceae L-Haloacid Dehalogenase Contains a Novel His/Glu Dyad that Could Activate the Catalytic Water. Authors: Novak, H.R. / Sayer, C. / Isupov, M.N. / Paszkiewicz, K. / Gotz, D. / Mearns Spragg, A. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yml.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yml.ent.gz | 90.9 KB | Display | PDB format |
PDBx/mmJSON format | 2yml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/2yml ftp://data.pdbj.org/pub/pdb/validation_reports/ym/2yml | HTTPS FTP |
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-Related structure data
Related structure data | 2ymmC 2ympC 2ymqC 2yn4C 2no4S C: citing same article (ref.) 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99986, -0.00994, 0.01334), Vector: |
-Components
#1: Protein | Mass: 25746.334 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTERACEAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIPL / References: UniProt: R4GRT2*PLUS #2: Water | ChemComp-HOH / | Sequence details | SEQUENCE MATCHES TO GENBANK JX868516 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→39.93 Å / Num. obs: 46369 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.79→1.83 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NO4 Resolution: 1.79→39.93 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.547 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.117 / 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: 22.925 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→39.93 Å
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Refine LS restraints |
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