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Yorodumi- PDB-1z74: Crystal Structure of E.coli ArnA dehydrogenase (decarboxylase) do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z74 | ||||||
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Title | Crystal Structure of E.coli ArnA dehydrogenase (decarboxylase) domain, R619Y mutant | ||||||
Components | protein ArnA | ||||||
Keywords | HYDROLASE / Rossmann fold | ||||||
Function / homology | Function and homology information UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding ...UDP-4-deoxy-4-formamido-beta-L-arabinopyranose biosynthetic process / UDP-glucuronic acid dehydrogenase activity / UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity / UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating) / UDP-4-amino-4-deoxy-L-arabinose formyltransferase / UDP-D-xylose biosynthetic process / UDP-glucuronate decarboxylase activity / lipopolysaccharide biosynthetic process / lipid A biosynthetic process / NAD+ binding / response to antibiotic / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Gatzeva-Topalova, P.Z. / May, A.P. / Sousa, M.C. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Structure and Mechanism of ArnA: Conformational Change Implies Ordered Dehydrogenase Mechanism in Key Enzyme for Polymyxin Resistance Authors: Gatzeva-Topalova, P.Z. / May, A.P. / Sousa, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z74.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z74.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 1z74.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z74_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 1z74_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 1z74_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1z74_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/1z74 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/1z74 | HTTPS FTP |
-Related structure data
Related structure data | 1z73C 1z75C 1z7bC 1z7eC 1u9jS 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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-Components
#1: Protein | Mass: 41490.172 Da / Num. of mol.: 1 / Fragment: dehydrogenase domain / Mutation: R619Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Description: plasmid is AN ENGINEERED VARIANT OF THE PET28 / Gene: PMRI, YFBG / Plasmid: PMS122 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3) / References: UniProt: P77398 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.7 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 2.0 M (NH4)2SO4, 5 MM DTT, 100 MM MES PH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 16479 / Num. obs: 16276 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1615 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U9J Resolution: 2.7→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2636425.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.5571 Å2 / ksol: 0.350088 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Xplor file |
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