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Yorodumi- PDB-6ltv: Crystal Structure of I122A/I330A variant of S-adenosylmethionine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ltv | ||||||
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Title | Crystal Structure of I122A/I330A variant of S-adenosylmethionine synthetase from Cryptosporidium hominis in complex with ONB-SAM (2-nitro benzyme S-adenosyl-methionine) | ||||||
Components | S-adenosylmethionine synthase | ||||||
Keywords | TRANSFERASE / Triphosphate / S-adenosylmethionine synthetase | ||||||
Function / homology | Function and homology information methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Cryptosporidium hominis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å | ||||||
Authors | Singh, R.K. / Michailidou, F. / Rentmeister, A. / Kuemmel, D. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021 Title: Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions. Authors: Michailidou, F. / Klocker, N. / Cornelissen, N.V. / Singh, R.K. / Peters, A. / Ovcharenko, A. / Kummel, D. / Rentmeister, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ltv.cif.gz | 317.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ltv.ent.gz | 255.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ltv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ltv_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6ltv_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 6ltv_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 6ltv_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/6ltv ftp://data.pdbj.org/pub/pdb/validation_reports/lt/6ltv | HTTPS FTP |
-Related structure data
Related structure data | 6ltwC 4odjS S: Starting model for refinement C: citing same article (ref.) |
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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: 45871.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Gene: CHUDEA7_2650 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0S4TKQ5, methionine adenosyltransferase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12.5 % MPD (v/v), 12.5 % PEG 1000 (w/v) , 12.5 % PEG 3350 (w/v), 0.1 MES/imidazole pH 6.5, 0.03 M sodium phosphate dibasic dihydrate, 0.03 M ammonium sulfate and 0.03 M sodium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→48.28 Å / Num. obs: 67224 / % possible obs: 99.1 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.041 / Rrim(I) all: 0.104 / Net I/σ(I): 15.2 / Num. measured all: 441998 / Scaling rejects: 1275 |
Reflection shell | Resolution: 1.87→1.92 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.776 / Num. unique obs: 4025 / CC1/2: 0.837 / Rpim(I) all: 0.327 / Rrim(I) all: 0.844 / % possible all: 91.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ODJ Resolution: 1.87→48.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.703 / SU ML: 0.088 / SU R Cruickshank DPI: 0.1278 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.118 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.56 Å2 / Biso mean: 29.952 Å2 / Biso min: 12.42 Å2
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Refinement step | Cycle: final / Resolution: 1.87→48.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.925 Å / Rfactor Rfree error: 0
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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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