+Open data
-Basic information
Entry | Database: PDB / ID: 1rw1 | ||||||
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Title | YFFB (PA3664) PROTEIN | ||||||
Components | conserved hypothetical protein yffB | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / thioredoxin fold / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.02 Å | ||||||
Authors | Teplyakov, A. / Pullalarevu, S. / Obmolova, G. / Doseeva, V. / Galkin, A. / Herzberg, O. / Dauter, M. / Dauter, Z. / Gilliland, G.L. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2004 Title: Crystal structure of the YffB protein from Pseudomonas aeruginosa suggests a glutathione-dependent thiol reductase function. Authors: Teplyakov, A. / Pullalarevu, S. / Obmolova, G. / Doseeva, V. / Galkin, A. / Herzberg, O. / Dauter, M. / Dauter, Z. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rw1.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rw1.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rw1_validation.pdf.gz | 424.7 KB | Display | wwPDB validaton report |
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Full document | 1rw1_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 1rw1_validation.xml.gz | 9 KB | Display | |
Data in CIF | 1rw1_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/1rw1 ftp://data.pdbj.org/pub/pdb/validation_reports/rw/1rw1 | 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: 13142.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: yffB / Plasmid: PET100-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q9HXX5 |
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#2: Chemical | ChemComp-IPA / |
#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: 2.09 Å3/Da / Density % sol: 41.04 % / Description: CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 295 K / pH: 10 Details: 0.1M CHES, 26% PEG 3350, 5% isopropanol, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 10.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9794 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 30, 2003 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→30 Å / Num. obs: 98866 / % possible obs: 91.2 % / Observed criterion σ(I): -4.5 / Redundancy: 3.9 % / Biso Wilson estimate: 8.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.02→1.04 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.6 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.02→15 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.264 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: ENGH & HUBER / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.02→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.02→1.05 Å / Total num. of bins used: 20 /
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