+Open data
-Basic information
Entry | Database: PDB / ID: 2fph | ||||||
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Title | Cell division protein ylmH from Streptococcus pneumoniae | ||||||
Components | ylmH | ||||||
Keywords | DNA BINDING PROTEIN / DIVISION PROTEIN / BACTERIA / GRAM+ | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å | ||||||
Authors | Garau, G. / Dideberg, O. | ||||||
Citation | Journal: To be Published Title: Cell division protein ylmH from Streptococcus pneumoniae Authors: Garau, G. / Job, V. / Dideberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fph.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fph.ent.gz | 33.8 KB | Display | PDB format |
PDBx/mmJSON format | 2fph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fph_validation.pdf.gz | 422.7 KB | Display | wwPDB validaton report |
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Full document | 2fph_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 2fph_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 2fph_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/2fph ftp://data.pdbj.org/pub/pdb/validation_reports/fp/2fph | 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: 19270.088 Da / Num. of mol.: 1 / Fragment: Residues 5-169 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (RIL) / References: GenBank: 15459167, UniProt: Q8DNW3*PLUS |
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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: 2.03 Å3/Da / Density % sol: 39.47 % |
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Crystal grow | Temperature: 293 K / pH: 5 Details: 10% PEG6000, 1.0M LiCl, 100mM citrate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9184 |
Detector | Type: MACSCIENCE / Detector: CCD / Date: Nov 17, 2005 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 17137 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.217 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.7→49.39 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 2.982 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.153 / ESU R Free: 0.154 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→49.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20 /
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