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- PDB-2ymp: Chloroacetic acid complex bound L-haloacid dehalogenase from a Rh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ymp | ||||||
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Title | Chloroacetic acid complex bound L-haloacid dehalogenase from a Rhodobacteraceae family bacterium | ||||||
![]() | L-HALOACID DEHALOGENASE | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Novak, H.R. / Sayer, C. / Isupov, M.N. / Paszkiewicz, K. / Gotz, D. / Spragg, A.M. / Littlechild, J.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.3 KB | Display | ![]() |
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PDB format | ![]() | 87.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.5 KB | Display | ![]() |
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Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 23.4 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ymlSC ![]() 2ymmC ![]() 2ymqC ![]() 2yn4C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99974, 0.02044, -0.0105), Vector: |
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Components
#1: Protein | Mass: 25804.369 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | SEQUENCE MATCHES TO GENBANK JX868516 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→42.3 Å / Num. obs: 33846 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.96→2.01 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YML Resolution: 1.96→40.91 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.714 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.146 / 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: 25.16 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→40.91 Å
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Refine LS restraints |
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