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Yorodumi- PDB-6r62: Crystal structure of a class II pyruvate aldolase from Sphingomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r62 | ||||||
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Title | Crystal structure of a class II pyruvate aldolase from Sphingomonas wittichii RW1 in complex with hydroxypyruvate | ||||||
Components | HpcH/HpaI aldolase | ||||||
Keywords | LYASE / Class II Pyruvate Aldolase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sphingomonas wittichii RW1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Marsden, S.R. / Mestrom, L. / Hagedoorn, P.L. / Bento, I. / McMillan, D.G.G. / Hanefeld, U. | ||||||
Citation | Journal: Adv.Synth.Catal. / Year: 2019 Title: CH-Pi Interactions Promote the Conversion of Hydroxypyruvate in a Class II Pyruvate Aldolase Authors: Marsden, S.R. / Mestrom, L. / Bento, I. / Hagedoorn, P.L. / McMillan, D.G.G. / Hanefeld, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r62.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r62.ent.gz | 130.2 KB | Display | PDB format |
PDBx/mmJSON format | 6r62.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/6r62 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/6r62 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 26784.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: the first two histidine residues are from the his-tag Source: (gene. exp.) Sphingomonas wittichii RW1 (bacteria) / Gene: Swit_5035 / Production host: Escherichia coli (E. coli) / References: UniProt: A5VH82 |
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-Non-polymers , 7 types, 374 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-MG / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NA / | #8: 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: 2.46 Å3/Da / Density % sol: 50.08 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion / Details: Sodium Citrate, Hepes |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL C/O DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2018 | ||||||||||||||||||||||||
Radiation | Monochromator: FMB-OXFORD DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.55→116.57 Å / Num. obs: 39857 / % possible obs: 100 % / Redundancy: 36.4 % / Biso Wilson estimate: 19.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.021 / Rrim(I) all: 0.124 / Net I/σ(I): 17 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.387
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→67.301 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→67.301 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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