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Yorodumi- PDB-4xt7: Crystal structure of Rv2671 from Mycobacterium tuberculosis in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xt7 | |||||||||
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Title | Crystal structure of Rv2671 from Mycobacterium tuberculosis in complex with NADP+ and trimethoprim | |||||||||
Components | Rv2671 | |||||||||
Keywords | OXIDOREDUCTASE / trimethoprim / reductase / Structural Genomics / TB Structural Genomics Consortium / TBSGC | |||||||||
Function / homology | Function and homology information 5-amino-6-(5-phosphoribosylamino)uracil reductase activity / riboflavin biosynthetic process / nucleotide binding / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Sacchettini, J.C. / Cheng, Y.S. / TB Structural Genomics Consortium (TBSGC) | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2016 Title: Structural Insights into Mycobacterium tuberculosis Rv2671 Protein as a Dihydrofolate Reductase Functional Analogue Contributing to para-Aminosalicylic Acid Resistance. Authors: Cheng, Y.S. / Sacchettini, J.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xt7.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xt7.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/4xt7 ftp://data.pdbj.org/pub/pdb/validation_reports/xt/4xt7 | HTTPS FTP |
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-Related structure data
Related structure data | 4xrbC 4xt4C 4xt5C 4xt6C 4xt8C 2p4gS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27721.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: ribD, Rv2671, RVBD_2671, LH57_14640, P425_02787 / Production host: Escherichia coli (E. coli) / References: UniProt: P71968 |
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-Non-polymers , 5 types, 70 molecules
#2: Chemical | ChemComp-NAP / |
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#3: Chemical | ChemComp-TOP / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-PEG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M sodium chloride, 25% PEG3350, 0.1M Bis-Tris pH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98011 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 11070 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.65 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.034 / Rrim(I) all: 0.092 / Χ2: 1.352 / Net I/av σ(I): 28.571 / Net I/σ(I): 9.2 / Num. measured all: 81136 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2p4g Resolution: 2.3→46.564 Å / FOM work R set: 0.8213 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.95 / 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 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.68 Å2 / Biso mean: 29.08 Å2 / Biso min: 11.53 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→46.564 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %
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