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Yorodumi- PDB-4mf4: Crystal structure of a HpcH/Hpal aldolase/citrate lyase family pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mf4 | ||||||
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Title | Crystal structure of a HpcH/Hpal aldolase/citrate lyase family protein from Burkholderia cenocepacia J2315 | ||||||
Components | HpcH/HpaI aldolase/citrate lyase family protein | ||||||
Keywords | LYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / aldolase / citrate lyase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia cenocepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a HpcH/Hpal aldolase/citrate lyase family protein from Burkholderia cenocepacia J2315 Authors: Lukacs, C.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mf4.cif.gz | 570.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mf4.ent.gz | 470.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/4mf4 ftp://data.pdbj.org/pub/pdb/validation_reports/mf/4mf4 | HTTPS FTP |
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-Related structure data
Related structure data | 1dxeS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28979.855 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: BceJ2315_04740, BCAL0476 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E7W8 #2: Chemical | ChemComp-EDO / #3: 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: 2.01 Å3/Da / Density % sol: 38.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: JCSG+a9: 20% PEG3350, 0.2M AmCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 95233 / Num. obs: 95110 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.15 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.15 / Num. unique all: 6950 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1DXE Resolution: 2→48.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.517 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.162 / 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: 21.775 Å2
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Refinement step | Cycle: LAST / Resolution: 2→48.95 Å
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