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Yorodumi- PDB-3ecd: Crystal structure of serine hydroxymethyltransferase from Burkhol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ecd | ||||||
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Title | Crystal structure of serine hydroxymethyltransferase from Burkholderia pseudomallei | ||||||
Components | Serine hydroxymethyltransferase 2 | ||||||
Keywords | TRANSFERASE / SSGCID / deCODE / BupsA00008a / One-carbon metabolism / Pyridoxal phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information glycine hydroxymethyltransferase / glycine hydroxymethyltransferase activity / glycine biosynthetic process from serine / tetrahydrofolate interconversion / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of serine hydroxymethyltransferase from Burkholderia pseudomallei Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ecd.cif.gz | 331.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ecd.ent.gz | 263.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ecd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ecd_validation.pdf.gz | 469.6 KB | Display | wwPDB validaton report |
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Full document | 3ecd_full_validation.pdf.gz | 484 KB | Display | |
Data in XML | 3ecd_validation.xml.gz | 69.7 KB | Display | |
Data in CIF | 3ecd_validation.cif.gz | 104.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/3ecd ftp://data.pdbj.org/pub/pdb/validation_reports/ec/3ecd | HTTPS FTP |
-Related structure data
Related structure data | 1kkjS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45586.688 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: glyA2, BPSS0547 / Production host: Escherichia coli (E. coli) References: UniProt: Q63MV1, UniProt: Q3JGP5*PLUS, glycine hydroxymethyltransferase #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Sequence details | THE TARGETDB ID BUPSA00008A DOES NOT EXIST IN TARGETDB AT THE TIME OF PROCESSING | |
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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: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PACT SCREEN CONDITION C6, 20% PEG 6000, 0.2 M NaCl, 0.1 M HEPES-KOH pH 7.0, 24.1 mg/mL protein, 0.4/0.4 uL drops, Crystal ID 109933C6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.99994 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Date: Aug 23, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99994 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→58.222 Å / Num. all: 408650 / Num. obs: 190206 / % possible obs: 94.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 12.358 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KKJ Resolution: 1.6→58.222 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.87 / SU B: 1.824 / SU ML: 0.064 / SU R Cruickshank DPI: 0.1 / SU Rfree: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 60.39 Å2 / Biso mean: 20.891 Å2 / Biso min: 6.86 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→58.222 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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