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Yorodumi- PDB-7ld8: Crystal Structure of Putative non-heme bromoperoxidase BpoC from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ld8 | ||||||
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Title | Crystal Structure of Putative non-heme bromoperoxidase BpoC from Mycobacterium tuberculosis H37Rv | ||||||
Components | Putative non-heme bromoperoxidase BpoC | ||||||
Keywords | OXIDOREDUCTASE / SSGCID / Putative non-heme bromoperoxidase / BpoC / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | bromide peroxidase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Putative non-heme bromoperoxidase BpoC Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: to be published Title: Crystal Structure of Putative non-heme bromoperoxidase BpoC from Mycobacterium tuberculosis H37Rv Authors: DeBouver, N.D. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ld8.cif.gz | 152.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ld8.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ld8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/7ld8 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/7ld8 | HTTPS FTP |
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-Related structure data
Related structure data | 3hssS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29448.588 Da / Num. of mol.: 1 / Fragment: MytuD.00095.b.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: bpoC, Rv0554 / Plasmid: MytuD.00095.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNH1, bromide peroxidase |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.37 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: MytuD.00095.b.B1.PW38899[Barcode: 318836d7, PuckID: neu1-3, Cryo: 20% EG, Concentration: 18 mg/mL] 100 mM Sodium Citrate/Citric Acid pH 5.5, 20% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 10, 2020 / Details: Beryllium Lenses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→50 Å / Num. obs: 38202 / % possible obs: 97.3 % / Redundancy: 7.164 % / Biso Wilson estimate: 22.769 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Χ2: 0.967 / Net I/σ(I): 28.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HSS Resolution: 1.5→43.37 Å / SU ML: 0.1153 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1257 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→43.37 Å
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Refine LS restraints |
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LS refinement shell |
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