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- PDB-4b5w: Crystal structures of divalent metal dependent pyruvate aldolase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b5w | |||||||||
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Title | Crystal structures of divalent metal dependent pyruvate aldolase R70A mutant, HpaI, in complex with pyruvate | |||||||||
![]() | 4-HYDROXY-2-OXO-HEPTANE-1,7-DIOATE ALDOLASE | |||||||||
![]() | LYASE | |||||||||
Function / homology | ![]() 4-hydroxy-2-ketopimelate aldolase activity / 4-hydroxy-2-oxoheptanedioate aldolase / : / phenylacetate catabolic process / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Coincon, M. / Wang, W. / Seah, S.Y.K. / Sygusch, J. | |||||||||
![]() | ![]() Title: Crystal Structure of Reaction Intermediates in Pyruvate Class II Aldolase: Substrate Cleavage, Enolate Stabilization and Substrate Specificity Authors: Coincon, M. / Wang, W. / Sygusch, J. / Seah, S.Y.K. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 576.1 KB | Display | ![]() |
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PDB format | ![]() | 480.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.1 KB | Display | ![]() |
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Full document | ![]() | 494.3 KB | Display | |
Data in XML | ![]() | 74.4 KB | Display | |
Data in CIF | ![]() | 109.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b5sC ![]() 4b5tC ![]() 4b5uC ![]() 4b5vC ![]() 4b5xC ![]() 2v5jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27366.146 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-256 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B1IS70, 2-dehydro-3-deoxyglucarate aldolase #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-PYR / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.7 % / Description: RPIM REPORTED INSTEAD OF RMERGE |
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Crystal grow | Details: 22% PEG 2000 MME, 10MM NICL2, 25MM HEPES PH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→38.5 Å / Num. obs: 127694 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 6.2 % / Biso Wilson estimate: 17.91 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4.8 / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2V5J Resolution: 1.792→38.493 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 17.15 / Stereochemistry target values: ML
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Displacement parameters | Biso mean: 21.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.792→38.493 Å
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Refine LS restraints |
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LS refinement shell |
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