+Open data
-Basic information
Entry | Database: PDB / ID: 1wa4 | ||||||
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Title | Crystal structure of the M131F L135A EvaD double mutant | ||||||
Components | PCZA361.16 | ||||||
Keywords | EPIMERASE / EVAD / AMYCOLATOPSIS ORIENTALIS / DOUBLE MUTANT / ORF24 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | AMYCOLATOPSIS ORIENTALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Merkel, A.B. / Naismith, J.H. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the M131F L135A Evad Double Mutant Authors: Merkel, A.B. / Naismith, J.H. #1: Journal: J.Biol.Chem. / Year: 2004 Title: The Position of a Key Tzrosine in Dtdp-4-Keto-6-Deoxy-D-Glucose-5-Epimerase (Evad) Alters the Substrate Profile for This Rmlc-Like Enzyme Authors: Merkel, A.B. / Major, L.L. / Errey, J.C. / Burkart, M.D. / Field, R.A. / Walsh, C.T. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wa4.cif.gz | 55.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wa4.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 1wa4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/1wa4 ftp://data.pdbj.org/pub/pdb/validation_reports/wa/1wa4 | HTTPS FTP |
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-Related structure data
Related structure data | 1ofnS 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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-Components
#1: Protein | Mass: 22485.596 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Strain: COSMID PCZA361 (AJ223998) / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52806 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | pH: 8 Details: 100MM TRIS, PH8, 150MM NACL, 25%W/V PEG8000, pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 14, 2003 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→48.22 Å / Num. obs: 9756 / % possible obs: 98.6 % / Observed criterion σ(I): 1.5 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.08→2.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.1 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OFN Resolution: 2.1→48.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.575 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.212 / 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: 13.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→48.22 Å
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Refine LS restraints |
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