+Open data
-Basic information
Entry | Database: PDB / ID: 2bmv | ||||||
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Title | Apoflavodoxin from Helicobacter pylori | ||||||
Components | FLAVODOXIN | ||||||
Keywords | ELECTRON TRANSPORT / FLAVOPROTEIN / HELICOBACTER PYLORI / FMN / TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | HELICOBACTER PYLORI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Martinez-Julvez, M. / Hermoso, J.A. / Sancho, J. / Perez-Dorado, I. / Cremades, N. / Bueno, M. | ||||||
Citation | 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. #1: Journal: Biophys.Chem. / Year: 2005 Title: Towards a Nwe Therapeutic Target: Helicobacter Pylori Flavodoxin Authors: Cremades, N. / Buen, 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 | 2bmv.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bmv.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 2bmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bmv_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
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Full document | 2bmv_full_validation.pdf.gz | 428.8 KB | Display | |
Data in XML | 2bmv_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 2bmv_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/2bmv ftp://data.pdbj.org/pub/pdb/validation_reports/bm/2bmv | 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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Unit cell |
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-Components
#1: Protein | Mass: 17512.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) Description: THE GENE THAT WAS EXPRESSED TO OBTAIN THE PROTEIN WAS ISOLATED FROM A PATIENT INFECTED WITH H.PYLORI SP. Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O25776 |
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#2: Chemical | ChemComp-BEN / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Sequence details | THE AUTHORS REPORT THAT DISCREPANCIES IN SEQUENCE ARE DUE TO THE FACT THAT THE GENE WAS ISOLATED ...THE AUTHORS REPORT THAT DISCREPANC |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.3 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: BRUCKER-NONIUS / Detector: CCD / Date: Oct 25, 2004 / Details: MONTEL MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→20.3 Å / Num. obs: 9402 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.17 / Rsym value: 0.17 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.11→2.18 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.56 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FUE Resolution: 2.11→9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.875 / SU B: 7.122 / SU ML: 0.184 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 19.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→9 Å
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Refine LS restraints |
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