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Yorodumi- PDB-2iqt: Crystal Structure of Fructose-Bisphosphate Aldolase, Class I from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iqt | ||||||
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Title | Crystal Structure of Fructose-Bisphosphate Aldolase, Class I from Porphyromonas gingivalis | ||||||
Components | Fructose-bisphosphate aldolase class 1 | ||||||
Keywords | LYASE / TIM berrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process Similarity search - Function | ||||||
Biological species | Porphyromonas gingivalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å | ||||||
Authors | Kim, Y. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Fructose-Bisphosphate Aldolase, Class I from Porphyromonas gingivalis Authors: Kim, Y. / Zhou, M. / Moy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iqt.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iqt.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 2iqt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iqt_validation.pdf.gz | 425.2 KB | Display | wwPDB validaton report |
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Full document | 2iqt_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 2iqt_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 2iqt_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/2iqt ftp://data.pdbj.org/pub/pdb/validation_reports/iq/2iqt | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33956.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: fbaB / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P60053, fructose-bisphosphate aldolase |
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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: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.2 M Ammonium citrate tribasic, 100 mM BTP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97869 |
Detector | Type: SBC-3 / Detector: CCD / Date: Dec 17, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→38.89 Å / Num. all: 16237 / Num. obs: 16237 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.44→2.53 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1602 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.46→38.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.105 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.452 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→38.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.457→2.521 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 26.4417 Å / Origin y: 31.1258 Å / Origin z: 61.6001 Å
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