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Yorodumi- PDB-4bk9: Crystal structure of 2-keto-3-deoxy-6-phospho-gluconate aldolase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bk9 | ||||||
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Title | Crystal structure of 2-keto-3-deoxy-6-phospho-gluconate aldolase from Zymomonas mobilis ATCC 29191 | ||||||
Components | 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE/4-HYDROXY-2-OXO GLUTARATE ALDOLASE | ||||||
Keywords | LYASE / ENTNER-DOUDOROFF-PATHWAY / CHEMOSELECTIVITY / PYRUVATE SPECIFICITY | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / : Function and homology information | ||||||
Biological species | ZYMOMONAS MOBILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | ||||||
Authors | Classen, T. / Schlieper, D. / Groth, G. / Pietruszka, J. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of 2-Keto-3-Deoxy-6-Phospho- Gluconate Aldolase from Zymomonas Mobilis Authors: Classen, T. / Schlieper, D. / Groth, G. / Pietruszka, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bk9.cif.gz | 236.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bk9.ent.gz | 192.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bk9_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
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Full document | 4bk9_full_validation.pdf.gz | 464.3 KB | Display | |
Data in XML | 4bk9_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 4bk9_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bk9 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bk9 | HTTPS FTP |
-Related structure data
Related structure data | 1fq0S 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: 22569.537 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ZYMOMONAS MOBILIS (bacteria) / Plasmid: PNHEDAZM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: I6XVB3, 2-dehydro-3-deoxy-phosphogluconate aldolase #2: Chemical | ChemComp-SO4 / #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: 2.6 Å3/Da / Density % sol: 52.25 % / Description: NONE |
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Crystal grow | Method: microbatch / pH: 4.6 Details: MICROBATCH, 1 UL 10 MG/ML PROTEIN PLUS 1 UL 100 MM NAOAC/ACOH PH 4.6, 200 MM (NH4)2SO4, 30% W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER 1-MICROS / Wavelength: 1.5418 |
Detector | Type: BRUKER / Detector: CCD / Date: Nov 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→59.03 Å / Num. obs: 15242 / % possible obs: 94.9 % / Observed criterion σ(I): 2.5 / Redundancy: 3.24 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.42 |
Reflection shell | Resolution: 2.77→2.85 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.53 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FQ0 Resolution: 2.77→7.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 19.499 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R Free: 0.272 / 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: 40.603 Å2
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Refinement step | Cycle: LAST / Resolution: 2.77→7.94 Å
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Refine LS restraints |
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