+Open data
-Basic information
Entry | Database: PDB / ID: 5a4j | ||||||
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Title | Crystal structure of FTHFS1 from T.acetoxydans Re1 | ||||||
Components | FORMATE--TETRAHYDROFOLATE LIGASE | ||||||
Keywords | LIGASE / PROTEIN | ||||||
Function / homology | Function and homology information formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / tetrahydrofolate interconversion / ATP binding Similarity search - Function | ||||||
Biological species | TEPIDANAEROBACTER ACETATOXYDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Bergdahl, R. / Jacobson, F. / Muller, B. / Mikkelsen, N. / Schurer, A. / Sandgren, M. | ||||||
Citation | Journal: To be Published Title: Characterization, Crystallization and Three- Dimensional Structures of Formyltetrahydrofolate Synthetase (Fthfs) from the Syntrophic Acetate Oxidising Bacterium Tepidanaerobacter Acetatoxydans Re1 Authors: Bergdahl, R. / Jacobson, F. / Muller, B. / Mikkelsen, N. / Schurer, A. / Sandgren, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a4j.cif.gz | 440 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a4j.ent.gz | 361.3 KB | Display | PDB format |
PDBx/mmJSON format | 5a4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a4j_validation.pdf.gz | 517.2 KB | Display | wwPDB validaton report |
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Full document | 5a4j_full_validation.pdf.gz | 535.4 KB | Display | |
Data in XML | 5a4j_validation.xml.gz | 83.7 KB | Display | |
Data in CIF | 5a4j_validation.cif.gz | 117.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/5a4j ftp://data.pdbj.org/pub/pdb/validation_reports/a4/5a4j | HTTPS FTP |
-Related structure data
Related structure data | 5a5gC 3rbo 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 60523.598 Da / Num. of mol.: 4 / Fragment: ENZYMATIC DOMAIN, UNP RESIDUES 1-559 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TEPIDANAEROBACTER ACETATOXYDANS (bacteria) Strain: RE1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: K7SWE7, formate-tetrahydrofolate ligase |
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-Non-polymers , 7 types, 975 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-K / #7: Chemical | ChemComp-ACT / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | AMINO ACID RESIDUE 372 HAS ACCIDENTALY BEEN MUTATED TO A THREONIN IN THE PROTEIN. NORMALLY IT IS AN ...AMINO ACID RESIDUE 372 HAS ACCIDENTAL |
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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: 2.34 Å3/Da / Density % sol: 47.49 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.20 M SODIUM-POTASSIUM TARTRATE 0.10 M BIS-TRIS PROPANE PH 6.5 18% W/V POLYETHYLENE GLYCOL (PEG) 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 1.04088 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04088 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→29.6 Å / Num. obs: 126940 / % possible obs: 98.9 % / Observed criterion σ(I): 3.8 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.7 / % possible all: 84.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RBO 3rbo Resolution: 2.15→29.62 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.854 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.187 / 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 mean: 34.625 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→29.62 Å
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Refine LS restraints |
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