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Yorodumi- PDB-2bkm: Crystal structure of the truncated hemoglobin from Geobacillus st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bkm | ||||||
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Title | Crystal structure of the truncated hemoglobin from Geobacillus stearothermophilus | ||||||
Components | TRUNCATED HEMOGLOBIN FROM GEOBACILLUS STEAROTHERMOPHILUS | ||||||
Keywords | OXYGEN STORAGE / HYPOTHETICAL PROTEIN / OXYGEN TRANSPORT / TRANSPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | GEOBACILLUS STEAROTHERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ilari, A. / Kjelgaard, P. / von Wachenfeldt, C. / Boffi, A. / Chiancone, E. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2007 Title: Crystal Structure and Ligand Binding Properties of the Truncated Hemoglobin from Geobacillus Stearothermophilus Authors: Ilari, A. / Kjelgaard, P. / von Wachenfeldt, C. / Catacchio, B. / Chiancone, E. / Boffi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bkm.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bkm.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bkm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2bkm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2bkm_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2bkm_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bkm ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bkm | HTTPS FTP |
-Related structure data
Related structure data | 1ux8S 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 domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 3 - 130 / Label seq-ID: 1 - 128
NCS oper: (Code: given Matrix: (-0.25347, -0.00705, 0.96732), Vector: |
-Components
#1: Protein | Mass: 14764.802 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Plasmid: PET101/D-TOPO / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: Q5L1S0 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 1.92 Å3/Da / Density % sol: 35.34 % |
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Crystal grow | pH: 5 Details: PEG 5000 MME 20-25 %, ACETATE BUFFER 0.1 M PH 5.2-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→40 Å / Num. obs: 36594 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.02 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UX8 Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.141 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→25 Å
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Refine LS restraints |
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