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Yorodumi- PDB-7cmy: Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cmy | ||||||
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Title | Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate | ||||||
Components | Isocitrate lyase | ||||||
Keywords | LYASE / Isocitrate lyase / Bacillus cereus / Glyoxylate cycle / Metal utilization enzyme | ||||||
Function / homology | Function and homology information isocitrate lyase / isocitrate lyase activity / carboxylic acid metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kim, K. / Ki, D. / Lee, S.H. | ||||||
Citation | Journal: To Be Published Title: Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate Authors: Kim, K. / Ki, D. / Lee, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cmy.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cmy.ent.gz | 138.3 KB | Display | PDB format |
PDBx/mmJSON format | 7cmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cmy_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 7cmy_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 7cmy_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 7cmy_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/7cmy ftp://data.pdbj.org/pub/pdb/validation_reports/cm/7cmy | HTTPS FTP |
-Related structure data
Related structure data | 3i4eS 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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Unit cell |
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-Components
#1: Protein | Mass: 47978.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria) Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: BC_1128 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q81GQ9, isocitrate lyase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.3 Å3/Da / Density % sol: 46.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50% PEG 400, 100mM CHES pH 9.5, 200mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 16, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 31543 / % possible obs: 98.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.086 / Rrim(I) all: 0.199 / Χ2: 3.343 / Net I/σ(I): 7.7 / Num. measured all: 168058 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I4E Resolution: 2.5→36.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.185 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.753 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 133.53 Å2 / Biso mean: 45.827 Å2 / Biso min: 24.74 Å2
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Refinement step | Cycle: final / Resolution: 2.5→36.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.56 Å / Rfactor Rfree error: 0
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