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Yorodumi- PDB-3g2q: Crystal Structure of the Glycopeptide N-methyltransferase MtfA co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g2q | ||||||
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Title | Crystal Structure of the Glycopeptide N-methyltransferase MtfA complexed with sinefungin | ||||||
Components | PCZA361.24 | ||||||
Keywords | TRANSFERASE / SAM-dependent methyltransferase / glycopeptide antibiotics biosynthesis / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI | ||||||
Function / homology | Function and homology information Carboxypeptidase Inhibitor; Chain A - #60 / HSP40/DNAj peptide-binding domain - #20 / : / HSP40/DNAj peptide-binding domain / Carboxypeptidase Inhibitor; Chain A / Methyltransferase domain 25 / Methyltransferase domain / Other non-globular / Vaccinia Virus protein VP39 / Special ...Carboxypeptidase Inhibitor; Chain A - #60 / HSP40/DNAj peptide-binding domain - #20 / : / HSP40/DNAj peptide-binding domain / Carboxypeptidase Inhibitor; Chain A / Methyltransferase domain 25 / Methyltransferase domain / Other non-globular / Vaccinia Virus protein VP39 / Special / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Amycolatopsis orientalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.18 Å | ||||||
Authors | Shi, R. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Chem.Biol. / Year: 2009 Title: Structure and function of the glycopeptide N-methyltransferase MtfA, a tool for the biosynthesis of modified glycopeptide antibiotics. Authors: Shi, R. / Lamb, S.S. / Zakeri, B. / Proteau, A. / Cui, Q. / Sulea, T. / Matte, A. / Wright, G.D. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g2q.cif.gz | 110.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g2q.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 3g2q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g2q_validation.pdf.gz | 1001.2 KB | Display | wwPDB validaton report |
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Full document | 3g2q_full_validation.pdf.gz | 1023.5 KB | Display | |
Data in XML | 3g2q_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 3g2q_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/3g2q ftp://data.pdbj.org/pub/pdb/validation_reports/g2/3g2q | HTTPS FTP |
-Related structure data
Related structure data | 3g2mSC 3g2oC 3g2pC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
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: 32527.627 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Gene: mtfA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O52805 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.55 Å3/Da / Density % sol: 51.77 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH 6.5, 18% PEG-monomethyl ether 5K, vapor diffusion, hanging drop, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 17, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→50 Å / Num. obs: 31659 / % possible obs: 92.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.043 / Χ2: 0.996 / Net I/σ(I): 22.896 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Starting model: PDB ENTRY 3G2M Resolution: 2.18→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.254 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.835 / SU B: 9.649 / SU ML: 0.13 / SU R Cruickshank DPI: 0.284 / SU Rfree: 0.201 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.262 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 116.01 Å2 / Biso mean: 50.357 Å2 / Biso min: 22.44 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.236 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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