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Yorodumi- PDB-6jbz: Structural analysis of molybdopterin synthases from two mycobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jbz | ||||||
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Title | Structural analysis of molybdopterin synthases from two mycobacteria pathogens | ||||||
Components |
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Keywords | TRANSFERASE / molybdopterin synthases / molybdenum cofactor biosynthesis / sulfur transfer | ||||||
Function / homology | Function and homology information molybdopterin synthase / molybdopterin synthase activity / Mo-molybdopterin cofactor biosynthetic process Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å | ||||||
Authors | Wang, H.Y. / Liu, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Structural analysis of molybdopterin synthases from two mycobacterial pathogens. Authors: Wang, H. / Chen, X. / Zhang, W. / Zhou, W. / Liu, X. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jbz.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jbz.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 6jbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/6jbz ftp://data.pdbj.org/pub/pdb/validation_reports/jb/6jbz | HTTPS FTP |
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-Related structure data
Related structure data | 6jc0C 2qieS 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: 15068.054 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: moaE2, DSI35_12490, ERS007665_01777, ERS023446_04125, ERS027644_03382, ERS027646_04529, ERS027651_03265, ERS027654_03076, ERS027656_02816, ERS027659_04568, ERS031537_04564, ERS124361_04403, ...Gene: moaE2, DSI35_12490, ERS007665_01777, ERS023446_04125, ERS027644_03382, ERS027646_04529, ERS027651_03265, ERS027654_03076, ERS027656_02816, ERS027659_04568, ERS031537_04564, ERS124361_04403, SAMEA2682864_02201, SAMEA2683035_02189 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A045HUW8, molybdopterin synthase #2: Protein | Mass: 9448.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: moaD2, DSI35_02305, ERS007661_02601, ERS007663_03167, ERS007665_02512, ERS007672_04797, ERS007679_03857, ERS007688_03620, ERS007703_04370, ERS007720_02994, ERS007722_03637, ERS007726_00134, ...Gene: moaD2, DSI35_02305, ERS007661_02601, ERS007663_03167, ERS007665_02512, ERS007672_04797, ERS007679_03857, ERS007688_03620, ERS007703_04370, ERS007720_02994, ERS007722_03637, ERS007726_00134, ERS007739_02763, ERS007741_03204, ERS023446_04078, ERS024213_03738, ERS024276_02321, ERS027644_02085, ERS027646_03803, ERS027651_01514, ERS027652_02678, ERS027653_03930, ERS027654_04370, ERS027659_02621, ERS027661_03197, ERS027666_05139, ERS031537_04168, ERS124361_05937, SAMEA2682864_02198, SAMEA2683035_02192 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A045H6C3 #3: Chemical | #4: 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: 4.03 Å3/Da / Density % sol: 69.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium chloride,BIS-TRIS,Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 24895 / % possible obs: 98.8 % / Redundancy: 25 % / Biso Wilson estimate: 41.75 Å2 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.038 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.6→2.68 Å / Redundancy: 24.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1993 / CC1/2: 0.96 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QIE Resolution: 2.603→47.03 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.603→47.03 Å
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Refine LS restraints |
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LS refinement shell |
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