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- PDB-4een: crystal structure of HAD FAMILY HYDROLASE DR_1622 from Deinococcu... -
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Basic information
Entry | Database: PDB / ID: 4een | ||||||
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Title | crystal structure of HAD FAMILY HYDROLASE DR_1622 from Deinococcus radiodurans R1 (TARGET EFI-501256) with bound magnesium | ||||||
![]() | Beta-phosphoglucomutase-related protein | ||||||
![]() | HYDROLASE / MAGNESIUM BINDING SITE / ENZYME FUNCTION INITIATIVE / Structural Genomics | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Allen, K.N. / Dunaway-Mariano, D. / Almo, S.C. / Enzyme Function Initiative (EFI) | ||||||
![]() | ![]() Title: Crystal structure of HAD HYDROLASE DR_1622 Deinococcus radiodurans R1 (TARGET EFI-501256) Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Allen, K. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Hillerich, B. / Seidel, R.D. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Zencheck, W.D. / Imker, H.J. / Allen, K.N. / Dunaway-Mariano, D. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.8 KB | Display | ![]() |
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PDB format | ![]() | 44.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.6 KB | Display | ![]() |
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Full document | ![]() | 433.1 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4eekSC ![]() 4eelC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 27538.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: DR_1622 / Production host: ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.69 % |
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Crystal grow | pH: 5.5 Details: 0.1M BIS-TRIS, PH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 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: 1.65→70 Å / Num. obs: 31336 / % possible obs: 98.4 % / Observed criterion σ(I): -5 / Redundancy: 16.2 % / Biso Wilson estimate: 25.925 Å2 / Rsym value: 0.1 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 18.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.91 / % possible all: 96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4EEK Resolution: 1.65→48.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.504 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.101 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.111 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→48.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.695 Å / Total num. of bins used: 20
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