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Yorodumi- PDB-7qcp: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qcp | ||||||
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Title | Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.2 - apo form | ||||||
Components | Glucosyl-3-phosphoglycerate synthase | ||||||
Keywords | TRANSFERASE / Glucose / UDP / thermostable / GTA-fold | ||||||
Function / homology | glucosyl-3-phosphoglycerate synthase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / L(+)-TARTARIC ACID / Glucosyl-3-phosphoglycerate synthase Function and homology information | ||||||
Biological species | Mycolicibacterium hassiacum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å | ||||||
Authors | Silva, A. / Nunes-Costa, D. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S. | ||||||
Funding support | Portugal, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Mycobacterium hassiacum glucosyl-3-phosphoglycerate synthase at pH 7.2 - apo form Authors: Silva, A. / Nunes-Costa, D. / Empadinhas, N. / Barbosa Pereira, P.J. / Macedo-Ribeiro, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qcp.cif.gz | 412 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qcp.ent.gz | 284.2 KB | Display | PDB format |
PDBx/mmJSON format | 7qcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/7qcp ftp://data.pdbj.org/pub/pdb/validation_reports/qc/7qcp | HTTPS FTP |
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-Related structure data
Related structure data | 7p5lS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35151.129 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The C-terminal KLAAALEHHHHHH sequence corresponds to a linker followed by an hexahistidine tag used for protein purification. Source: (gene. exp.) Mycolicibacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria) Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: gpgS, C731_3243, MHAS_02845 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: K5B7Z4, glucosyl-3-phosphoglycerate synthase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.19 Å3/Da / Density % sol: 43.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.2M Potassium Sodium Tartrate pH 7.2, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96112 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96112 Å / Relative weight: 1 |
Reflection | Resolution: 1.11→50 Å / Num. obs: 242579 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 12.18 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.069 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.11→1.15 Å / Rmerge(I) obs: 1.116 / Mean I/σ(I) obs: 2 / Num. unique obs: 23553 / Rpim(I) all: 0.371 / Rrim(I) all: 1.178 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7P5L Resolution: 1.11→47.65 Å / SU ML: 0.1134 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.2344 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.11→47.65 Å
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Refine LS restraints |
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LS refinement shell |
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