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Yorodumi- PDB-6q62: Xanthomonas albilineans Dihydropteroate synthase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q62 | ||||||
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Title | Xanthomonas albilineans Dihydropteroate synthase in complex with (indole-2-carboxylic acid) and (6-chloroguanine) | ||||||
Components | Dihydropteroate synthase | ||||||
Keywords | TRANSFERASE / Complex / FBDD / Fragments | ||||||
Function / homology | Function and homology information dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Xanthomonas albilineans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Oliveira, A.A. / Hyvonen, M. / Guido, R.V.C. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Xanthomonas albilineans Dihydropteroate synthase in complex with (indole-2-carboxylic acid) and (6-chloroguanine) Authors: Oliveira, A.A. / Hyvonen, M. / Guido, R.V.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q62.cif.gz | 227.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q62.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 6q62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q62_validation.pdf.gz | 520.4 KB | Display | wwPDB validaton report |
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Full document | 6q62_full_validation.pdf.gz | 531.8 KB | Display | |
Data in XML | 6q62_validation.xml.gz | 47.1 KB | Display | |
Data in CIF | 6q62_validation.cif.gz | 68.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/6q62 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/6q62 | HTTPS FTP |
-Related structure data
Related structure data | 6dayS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ACBD
#1: Protein | Mass: 31883.580 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas albilineans (bacteria) / Gene: folP, XALc_1165 / Plasmid: pETTrx / Details (production host): Thioredoxin + 6xHis / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): T7Lac / References: UniProt: D2UDM3, dihydropteroate synthase |
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-Non-polymers , 6 types, 803 molecules
#2: Chemical | ChemComp-6GU / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: 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: 2.11 Å3/Da / Density % sol: 43 % / Description: Monoclinic |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3.350, Li2SO4, Bis-tris |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: Liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→54 Å / Num. obs: 137050 / % possible obs: 81.84 % / Redundancy: 6.9 % / Biso Wilson estimate: 17.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08753 / Rpim(I) all: 0.03612 / Rrim(I) all: 0.09483 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 1.6→1.657 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 5075 / CC1/2: 0.75 / % possible all: 36.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DAY Resolution: 1.5→42.09 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.107
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Displacement parameters | Biso mean: 23.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.5→42.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 Å / Total num. of bins used: 20
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