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Yorodumi- PDB-6wyc: Crystal Structure of Chlamydia trachomatis Glyceraldehyde 3-phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wyc | ||||||
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Title | Crystal Structure of Chlamydia trachomatis Glyceraldehyde 3-phosphate dehydrogenase | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / GAPDH / NAD / Glycolysis / Chlamydia | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Chlamydia trachomatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Schormann, N. / Chattopadhyay, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2020 Title: Chlamydia trachomatis glyceraldehyde 3-phosphate dehydrogenase: Enzyme kinetics, high-resolution crystal structure, and plasminogen binding. Authors: Schormann, N. / Campos, J. / Motamed, R. / Hayden, K.L. / Gould, J.R. / Green, T.J. / Senkovich, O. / Banerjee, S. / Ulett, G.C. / Chattopadhyay, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wyc.cif.gz | 291.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wyc.ent.gz | 235.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/6wyc ftp://data.pdbj.org/pub/pdb/validation_reports/wy/6wyc | HTTPS FTP |
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-Related structure data
Related structure data | 6x2eC 4qx6S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 36418.605 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The protein is modified at two cysteine positions (63 and 287). Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria) Strain: D/UW-3/Cx / Gene: gap, gapA, CT_505 / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0CE13, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NAD / #3: 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: 1.98 Å3/Da / Density % sol: 37.8 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 2000 MME, 0.1 M Hepes, pH 7.5; prior to crystallization the protein (at 30 mg/ml) was incubated with 1 mM NAD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→66.26 Å / Num. obs: 173217 / % possible obs: 93.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.045 / Rrim(I) all: 0.089 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.626 / Num. unique obs: 8596 / CC1/2: 0.679 / Rpim(I) all: 0.388 / Rrim(I) all: 0.742 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QX6 Resolution: 1.5→66.26 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.618 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.079 / 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: 68.73 Å2 / Biso mean: 17.1 Å2 / Biso min: 5.5 Å2
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Refinement step | Cycle: final / Resolution: 1.5→66.26 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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