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Yorodumi- PDB-2bvc: Crystal structure of Mycobacterium tuberculosis glutamine synthet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bvc | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition state mimic | ||||||
Components | GLUTAMINE SYNTHETASE 1 | ||||||
Keywords | LIGASE / TRANSITION STATE MIMIC / SYNTHETASE | ||||||
Function / homology | Function and homology information nitrogen utilization / positive regulation of plasminogen activation / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / cell wall / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization ...nitrogen utilization / positive regulation of plasminogen activation / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / cell wall / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization / magnesium ion binding / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Krajewski, W.W. / Jones, T.A. / Mowbray, S.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Structure of Mycobacterium Tuberculosis Glutamine Synthetase in Complex with a Transition-State Mimic Provides Functional Insights. Authors: Krajewski, W.W. / Jones, T.A. / Mowbray, S.L. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bvc.cif.gz | 568 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bvc.ent.gz | 464.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bvc_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 2bvc_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 2bvc_validation.xml.gz | 99 KB | Display | |
Data in CIF | 2bvc_validation.cif.gz | 137.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/2bvc ftp://data.pdbj.org/pub/pdb/validation_reports/bv/2bvc | HTTPS FTP |
-Related structure data
Related structure data | 1htoS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 6 / Auth seq-ID: 4 - 478 / Label seq-ID: 12 - 486
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 54584.730 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCR T7/CT-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P0A590, UniProt: P9WN39*PLUS, glutamine synthetase |
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-Non-polymers , 5 types, 657 molecules
#2: Chemical | ChemComp-P3S / #3: Chemical | ChemComp-ADP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CL / #6: 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: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 6.8 / Details: 30% PEG400, 0.1M MES PH6.8, 200 MM MGCL2, pH 6.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 3, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 160432 / % possible obs: 89.6 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.4 / % possible all: 69.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HTO Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.036 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.2 / 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: 25.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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