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Yorodumi- PDB-3hl0: Crystal structure of Maleylacetate reductase from Agrobacterium t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hl0 | ||||||
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Title | Crystal structure of Maleylacetate reductase from Agrobacterium tumefaciens | ||||||
Components | Maleylacetate reductase | ||||||
Keywords | OXIDOREDUCTASE / maleylacetate reductase / Agrobacterium tumefaciens / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information maleylacetate reductase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Chang, C. / Evdokimova, E. / Mursleen, A. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Maleylacetate reductase from Agrobacterium tumefaciens Authors: Chang, C. / Evdokimova, E. / Mursleen, A. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hl0.cif.gz | 153.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hl0.ent.gz | 128.6 KB | Display | PDB format |
PDBx/mmJSON format | 3hl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hl0_validation.pdf.gz | 731 KB | Display | wwPDB validaton report |
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Full document | 3hl0_full_validation.pdf.gz | 738.3 KB | Display | |
Data in XML | 3hl0_validation.xml.gz | 33 KB | Display | |
Data in CIF | 3hl0_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/3hl0 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/3hl0 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37100.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Strain: C58 / Gene: macA, AGR_C_4594, Atu2528 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9CHP3 #2: Chemical | #3: Chemical | ChemComp-NAD / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.23 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Calcium chloride dihydrate, 0.1M HEPES pH7.5, 28% P400, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97962 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 20, 2009 |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97962 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 84140 / Num. obs: 84095 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 44.9 |
Reflection shell | Resolution: 1.6→1.61 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 5.37 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→28.84 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.929 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 15.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.643 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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