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Yorodumi- PDB-6voq: Crystal structure of YgbL, a putative aldolase/epimerase/decarbox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6voq | ||||||
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Title | Crystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Klebsiella pneumoniae | ||||||
Components | AldolaseFructose-bisphosphate aldolase | ||||||
Keywords | LYASE / PUTATIVE LYASE / EPIMERASE / ALDOLASE / ISOMERASE / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES | ||||||
Function / homology | L-fuculose-phosphate aldolase / L-fuculose-phosphate aldolase activity / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / Aldolase Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Stogios, P.J. / Evdokimova, E. / McChesney, C. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of YgbL, a putative aldolase/epimerase/decarboxylase from Klebsiella pneumoniae Authors: Stogios, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6voq.cif.gz | 117.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6voq.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 6voq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vo/6voq ftp://data.pdbj.org/pub/pdb/validation_reports/vo/6voq | HTTPS FTP |
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-Related structure data
Related structure data | 2opiS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22707.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: fucA_2, fucA_1, fucA_3, BL124_00025510, C3483_13535, C3F39_01215, C7V41_22435, CWN54_08000, DD581_15345, DM059_14180, EAO17_27025, EXT45_05660, FAM48_01070, FAQ72_03260, FAQ97_05405, FAS39_ ...Gene: fucA_2, fucA_1, fucA_3, BL124_00025510, C3483_13535, C3F39_01215, C7V41_22435, CWN54_08000, DD581_15345, DM059_14180, EAO17_27025, EXT45_05660, FAM48_01070, FAQ72_03260, FAQ97_05405, FAS39_03255, FNY87_25290, NCTC11679_02859, NCTC13465_01855, NCTC1936_02659, NCTC5047_00576, NCTC9140_04285, NCTC9601_02686, NCTC9645_06176, NCTC9661_03377, PMK1_03924, SAMEA24002668_05560, SAMEA4364603_02467, SK89_00182 Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic / References: UniProt: Q0QC76, L-fuculose-phosphate aldolase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2M Na Tartrate, 0.1M TRIS pH 8.5, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 31, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→25 Å / Num. obs: 9859 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 35.89 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.037 / Net I/σ(I): 18.74 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 2.59 / Num. unique obs: 490 / CC1/2: 0.91 / Rpim(I) all: 0.233 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OPI Resolution: 2.49→24.58 Å / SU ML: 0.2477 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.2302
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.49→24.58 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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