+Open data
-Basic information
Entry | Database: PDB / ID: 3ios | |||||||||
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Title | Structure of MTB dsbF in its mixed oxidized and reduced forms | |||||||||
Components | Disulfide bond forming protein (DsbF) | |||||||||
Keywords | OXIDOREDUCTASE / thioredoxin fold / disulfide bond forming protein / isomerase / Lipoprotein | |||||||||
Function / homology | Function and homology information thiol oxidase activity / : / antioxidant activity / cell redox homeostasis Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.6 Å | |||||||||
Authors | Chim, N. / Goulding, C.W. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: An extracellular disulfide bond forming protein (DsbF) from Mycobacterium tuberculosis: structural, biochemical, and gene expression analysis. Authors: Chim, N. / Riley, R. / The, J. / Im, S. / Segelke, B. / Lekin, T. / Yu, M. / Hung, L.W. / Terwilliger, T. / Whitelegge, J.P. / Goulding, C.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ios.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ios.ent.gz | 28.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ios.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ios_validation.pdf.gz | 404.5 KB | Display | wwPDB validaton report |
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Full document | 3ios_full_validation.pdf.gz | 405.4 KB | Display | |
Data in XML | 3ios_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | 3ios_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/3ios ftp://data.pdbj.org/pub/pdb/validation_reports/io/3ios | HTTPS FTP |
-Related structure data
Related structure data | 1lu4S 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: 16430.303 Da / Num. of mol.: 1 / Fragment: UNP residues 47-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dsbF, MT1716, Rv1677 / Plasmid: PETT7 / Production host: Escherichia coli (E. coli) / References: UniProt: O53924 |
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#2: 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: 2.29 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 0.1 M NA malonate ph 7.0, 2.04 M NA citrate, 5% LDAO, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9786 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2003 |
Radiation | Monochromator: DOUBLE CRYSTAL SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 23073 / % possible obs: 100 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 40.68 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 3.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 1LU4 Resolution: 1.6→10 Å / Num. parameters: 10398 / Num. restraintsaints: 13025 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 233 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1130 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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