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Yorodumi- PDB-2x5s: Crystal structure of T. maritima GDP-mannose pyrophosphorylase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x5s | ||||||
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Title | Crystal structure of T. maritima GDP-mannose pyrophosphorylase in apo state. | ||||||
Components | MANNOSE-1-PHOSPHATE GUANYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / NUCLEOTIDYL TRANSFERASE | ||||||
Function / homology | Function and homology information mannose-1-phosphate guanylyltransferase (GTP) activity / GDP-mannose biosynthetic process / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | THERMOTOGA MARITIMA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Pelissier, M.C. / Lesley, S. / Kuhn, P. / Bourne, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural Insights Into the Catalytic Mechanism of Bacterial Guanosine-Diphospho-D-Mannose Pyrophosphorylase and its Regulation by Divalent Ions. Authors: Pelissier, M.C. / Lesley, S. / Kuhn, P. / Bourne, Y. | ||||||
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 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x5s.cif.gz | 145 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x5s.ent.gz | 114.5 KB | Display | PDB format |
PDBx/mmJSON format | 2x5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/2x5s ftp://data.pdbj.org/pub/pdb/validation_reports/x5/2x5s | HTTPS FTP |
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-Related structure data
Related structure data | 2x5zC 2x60C 2x65C 2cu2S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38655.359 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: MSB8 / Description: DSM 3109 / Plasmid: PMH1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ORIGAMI (DE3) PLYSS References: UniProt: Q9X0C3, mannose-1-phosphate guanylyltransferase #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, MET 1 TO VAL ENGINEERED RESIDUE IN CHAIN A, VAL 261 TO LEU ...ENGINEERED | |
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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: 2.43 Å3/Da / Density % sol: 49.47 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 MM PCB PH 7.5, 35% (V/V) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→65.37 Å / Num. obs: 31744 / % possible obs: 99.2 % / Observed criterion σ(I): 3.5 / Redundancy: 6 % / Biso Wilson estimate: 59.338 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CU2 Resolution: 2.35→65.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / SU B: 23.518 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.786 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→65.37 Å
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