+Open data
-Basic information
Entry | Database: PDB / ID: 3cht | ||||||
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Title | Crystal Structure of Di-iron AurF with partially bound Ligand | ||||||
Components | p-Aminobenzoate N-Oxygenase | ||||||
Keywords | OXIDOREDUCTASE / Di-iron oxygenase | ||||||
Function / homology | Function and homology information 4-aminobenzoate N-oxygenase / oxidoreductase activity / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces thioluteus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhang, H. / Brunzelle, J.S. / Nair, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: In vitro reconstitution and crystal structure of p-aminobenzoate N-oxygenase (AurF) involved in aureothin biosynthesis. Authors: Choi, Y.S. / Zhang, H. / Brunzelle, J.S. / Nair, S.K. / Zhao, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cht.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cht.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 3cht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cht_validation.pdf.gz | 462 KB | Display | wwPDB validaton report |
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Full document | 3cht_full_validation.pdf.gz | 472.3 KB | Display | |
Data in XML | 3cht_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 3cht_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/3cht ftp://data.pdbj.org/pub/pdb/validation_reports/ch/3cht | HTTPS FTP |
-Related 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: 38129.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces thioluteus (bacteria) / Gene: aurF / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q70KH9 #2: Chemical | #3: Chemical | ChemComp-4NB / | #4: 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: 2.07 Å3/Da / Density % sol: 40.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 18-22% PEG 8000, 50 mM Tris-HCl, soaked in 5 mM pNBA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 42156 / Num. obs: 39867 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Redundancy: 4.5 % / Rsym value: 0.075 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4065 / Rsym value: 0.423 / % possible all: 95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.574 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.187 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.711 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 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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