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Yorodumi- PDB-2w5u: Flavodoxin from Helicobacter pylori in complex with the C3 inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w5u | ||||||
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Title | Flavodoxin from Helicobacter pylori in complex with the C3 inhibitor | ||||||
Components | Flavodoxin | ||||||
Keywords | ELECTRON TRANSPORT / DRUG DISCOVERY / PROTEIN HINHIBITOR / FMN / TRANSPORT / FLAVODOXIN / FLAVOPROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Cremades, N. / Perez-Dorado, I. / Hermoso, J.A. / Martinez-Julvez, M. / Sancho, J. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2009 Title: Discovery of Specific Flavodoxin Inhibitors as Potential Therapeutic Agents Against Helicobacter Pylori Infection. Authors: Cremades, N. / Velazquez-Campoy, A. / Martinez-Julvez, M. / Neira, J.L. / Perez-Dorado, I. / Hermoso, J. / Jimenez, P. / Lanas, A. / Hoffman, P.S. / Sancho, J. #1: Journal: Proteins / Year: 2007 Title: Common Conformational Changes in Flavodoxins Induced by Fmn and Anion Binding: The Structure of Helicobacter Pylori Apoflavodoxin. Authors: Martinez-Julvez, M. / Cremades, N. / Bueno, M. / Perez-Dorado, I. / Maya, C. / Cuesta-Lopez, S. / Prada, D. / Falo, F. / Hermoso, J.A. / Sancho, J. #2: Journal: Biophys.Chem. / Year: 2005 Title: Towards a New Therapeutic Target: Helicobacter Pylori Flavodoxin. Authors: Cremades, N. / Bueno, M. / Toja, M. / Sancho, J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w5u.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w5u.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 2w5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w5u_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2w5u_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2w5u_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 2w5u_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/2w5u ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w5u | HTTPS FTP |
-Related structure data
Related structure data | 1fueS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9559, -0.0105, -0.2936), Vector: |
-Components
#1: Protein | Mass: 17540.322 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Plasmid: PET28A-FLDA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O25776 #2: Chemical | #3: Chemical | ChemComp-IC3 / [ | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE CONFLICTS LISTED IN THE SEQADV RECORDS BELOW ARE DUE TO THE FACT THAT THE PROTEIN ...THE SEQUENCE CONFLICTS LISTED IN THE SEQADV RECORDS BELOW ARE DUE TO THE FACT THAT THE PROTEIN SEQUENCE WAS OBTAINED DIRECTLY FROM THE H.PYLORI BACTERIA OF A PATIENT. | |
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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: 2.1 Å3/Da / Density % sol: 40.8 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS / Detector: CCD / Date: May 10, 2008 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→22 Å / Num. obs: 8523 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.9 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FUE Resolution: 2.62→22 Å / Cross valid method: THROUGHOUT Details: AFTER MODEL REFINEMENT WITH CNS PROGRAM A LAST CYCLE OF REFINEMENT WAS PERFORMED USING REFMAC5 WITH TLS. INITIAL METEONINE RESIDUE WAS NOT OBSERVED NEITHER IN MOLECULE A NOR IN MOLECULE B
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.69 Å / Rfactor Rfree: 0.306 / Rfactor Rwork: 0.283 / Total num. of bins used: 20 |