+Open data
-Basic information
Entry | Database: PDB / ID: 2w31 | ||||||
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Title | globin domain of Geobacter sulfurreducens globin-coupled sensor | ||||||
Components | GLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / GEOBACTER SULFURREDUCENS / HEXACOORDINATION / GLOBIN COUPLED SENSOR | ||||||
Function / homology | Function and homology information oxygen binding / membrane => GO:0016020 / heme binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | GEOBACTER SULFURREDUCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Pesce, A. / Thijs, L. / Nardini, M. / Desmet, F. / Sisinni, L. / Gourlay, L. / Bolli, A. / Coletta, M. / Van Doorslaer, S. / Wan, X. ...Pesce, A. / Thijs, L. / Nardini, M. / Desmet, F. / Sisinni, L. / Gourlay, L. / Bolli, A. / Coletta, M. / Van Doorslaer, S. / Wan, X. / Alam, M. / Ascenzi, P. / Moens, L. / Bolognesi, M. / Dewilde, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Hise11 and Hisf8 Provide Bis-Histidyl Heme Hexa-Coordination in the Globin Domain of Geobacter Sulfurreducens Globin-Coupled Sensor. Authors: Pesce, A. / Thijs, L. / Nardini, M. / Desmet, F. / Sisinni, L. / Gourlay, L. / Bolli, A. / Coletta, M. / Van Doorslaer, S. / Wan, X. / Alam, M. / Ascenzi, P. / Moens, L. / Bolognesi, M. / Dewilde, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w31.cif.gz | 157 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w31.ent.gz | 132.7 KB | Display | PDB format |
PDBx/mmJSON format | 2w31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w31_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 2w31_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 2w31_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 2w31_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/2w31 ftp://data.pdbj.org/pub/pdb/validation_reports/w3/2w31 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19190.734 Da / Num. of mol.: 2 Fragment: GLOBIN DOMAIN OF GLOBIN COUPLED SENSOR, RESIDUES 1-162 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACTER SULFURREDUCENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q747F6 #2: Chemical | #3: Chemical | #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: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | Temperature: 277 K / pH: 6.5 Details: 10% PEG 4000, 0.1 M MES PH 6.5, 0.2 M MGCL2, AT 277 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.837 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.837 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.4 Å / Num. obs: 60673 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.5→34.14 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.43 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES FROM 153 TO 162 WERE DISORDERED AND WERE NOT MODELLED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→34.14 Å
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Refine LS restraints |
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