+Open data
-Basic information
Entry | Database: PDB / ID: 1zgh | |||||||||
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Title | Methionyl-tRNA formyltransferase from Clostridium thermocellum | |||||||||
Components | Methionyl-tRNA formyltransferase | |||||||||
Keywords | TRANSFERASE / Methionyl-tRNA formyltransferase / Southeast Collaboratory for Structural Genomics / Clostridium thermocellum / PSI / Protein Structure Initiative / SECSG | |||||||||
Function / homology | Function and homology information hydroxymethyl-, formyl- and related transferase activity / biosynthetic process Similarity search - Function | |||||||||
Biological species | Clostridium thermocellum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 2.05 Å | |||||||||
Authors | Yang, H. / Kataeva, I. / Xu, H. / Zhao, M. / Chang, J. / Liu, Z. / Chen, L. / Tempel, W. / Habel, J. / Zhou, W. ...Yang, H. / Kataeva, I. / Xu, H. / Zhao, M. / Chang, J. / Liu, Z. / Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Lee, D. / Lin, D. / Chang, S. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Wang, B. / Southeast Collaboratory for Structural Genomics (SECSG) | |||||||||
Citation | Journal: To be published Title: Methionyl-tRNA formyltransferase from Clostridium thermocellum Authors: Yang, H. / Kataeva, I. / Xu, H. / Zhao, M. / Chang, J. / Liu, Z. / Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Lee, D. / Lin, D. / Chang, S. / Arendall III, W.B. / Richardson, J.S. / ...Authors: Yang, H. / Kataeva, I. / Xu, H. / Zhao, M. / Chang, J. / Liu, Z. / Chen, L. / Tempel, W. / Habel, J. / Zhou, W. / Lee, D. / Lin, D. / Chang, S. / Arendall III, W.B. / Richardson, J.S. / Richardson, D.C. / Rose, J.P. / Wang, B. / Southeast Collaboratory for Structural Genomics | |||||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S).AUTHOR STATES THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zgh.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zgh.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1zgh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zgh_validation.pdf.gz | 401.8 KB | Display | wwPDB validaton report |
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Full document | 1zgh_full_validation.pdf.gz | 401.8 KB | Display | |
Data in XML | 1zgh_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 1zgh_validation.cif.gz | 9.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zg/1zgh ftp://data.pdbj.org/pub/pdb/validation_reports/zg/1zgh | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30354.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Plasmid: pET-15g / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 48859327, UniProt: A3DHJ7*PLUS | ||
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#2: Chemical | ChemComp-UNX / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 298 K / Method: modified microbatch / pH: 5.6 Details: 2.5M amonium sulfate, 0.1M sodium citrate, pH 5.6, modified microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→50 Å / Num. obs: 27555 / % possible obs: 98.3 % / Rmerge(I) obs: 0.118 / Χ2: 2.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: sad | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD | D res high: 2.5 Å / D res low: 20 Å / FOM : 0.4 / Reflection: 13589 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD shell |
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Phasing dm | FOM : 0.58 / FOM acentric: 0.59 / FOM centric: 0.51 / Reflection: 17127 / Reflection acentric: 14644 / Reflection centric: 2483 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAS / Resolution: 2.05→30.192 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.213 / SU B: 6.361 / SU ML: 0.088 / SU R Cruickshank DPI: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.139 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; arp/warp,molprobity were also used in refinement
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.984 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→30.192 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 33.312 Å / Origin y: 27.772 Å / Origin z: 31.685 Å
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Refinement TLS group | Selection: ALL |