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Yorodumi- PDB-3dki: 2.1 A X-ray structure of CysM (Rv1336) from Mycobacterium tubercu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dki | ||||||
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Title | 2.1 A X-ray structure of CysM (Rv1336) from Mycobacterium tuberculosis an O-phosphoserine dependent cysteine synthase | ||||||
Components | Cysteine synthase B | ||||||
Keywords | TRANSFERASE / Cysteine synthase / O-phosphoserine / CysO(Rv1335) / Pyridoxal-phosphate / PLP / Amino-acid biosynthesis / Cysteine biosynthesis / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase / Cysteine synthesis from O-phosphoserine / O-phosphoserine sulfhydrylase activity / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process / cysteine biosynthetic process from serine / pyridoxal phosphate binding / protein-containing complex / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Agren, D. / Schnell, R. / Schneider, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Cysteine Synthase (CysM) of Mycobacterium tuberculosis Is an O-Phosphoserine Sulfhydrylase: EVIDENCE FOR AN ALTERNATIVE CYSTEINE BIOSYNTHESIS PATHWAY IN MYCOBACTERIA Authors: Agren, D. / Schnell, R. / Oehlmann, W. / Singh, M. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dki.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dki.ent.gz | 100.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/3dki ftp://data.pdbj.org/pub/pdb/validation_reports/dk/3dki | HTTPS FTP |
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-Related structure data
Related structure data | 2q3bS 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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Unit cell |
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-Components
#1: Protein | Mass: 34952.234 Da / Num. of mol.: 2 / Mutation: T2A Source method: isolated from a genetically manipulated source Details: N-terminal His6-tag removed by Thrombin cleavage / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: cysM, Rv1336 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P63873, UniProt: P9WP53*PLUS, O-phosphoserine sulfhydrylase #2: Chemical | ChemComp-NA / | #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: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Tris-HCl pH 7.5, 0.1M K2HPO4, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008 Details: Channel cut ESRF monochromator, Torodial focusing mirror |
Radiation | Monochromator: Channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 38897 / Num. obs: 38431 / % possible obs: 98.8 % / Observed criterion σ(I): 2.6 / Redundancy: 3.1 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.085 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5613 / Rsym value: 0.539 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q3B Resolution: 2.1→28.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.198 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(I): 2.6 / ESU R: 0.215 / ESU R Free: 0.188 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.102 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→28.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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