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Yorodumi- PDB-4pmr: Crystal structure of the Mycobacterium tuberculosis Tat-secreted ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pmr | ||||||
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Title | Crystal structure of the Mycobacterium tuberculosis Tat-secreted protein Rv2525c in complex with HEPES (monoclinic crystal form II) | ||||||
Components | Tat-secreted protein Rv2525c | ||||||
Keywords | UNKNOWN FUNCTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Bellinzoni, M. / Haouz, A. / Shepard, W. / Alzari, P.M. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2014 Title: Structural studies suggest a peptidoglycan hydrolase function for the Mycobacterium tuberculosis Tat-secreted protein Rv2525c. Authors: Bellinzoni, M. / Haouz, A. / Miras, I. / Magnet, S. / Andre-Leroux, G. / Mukherjee, R. / Shepard, W. / Cole, S.T. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pmr.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pmr.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 4pmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/4pmr ftp://data.pdbj.org/pub/pdb/validation_reports/pm/4pmr | HTTPS FTP |
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-Related structure data
Related structure data | 4pmnSC 4pmoC 4pmqC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 22043.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: MT2601 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P95028 |
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#2: Chemical | ChemComp-EPE / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.26 M tri-sodium citrate, 90 mM Hepes-Na pH 7.5, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9198 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9198 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→48.56 Å / Num. obs: 16674 / % possible obs: 98.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 16.49 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.916 / Mean I/σ(I) obs: 1.2 / % possible all: 82.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PMN Resolution: 1.81→48.56 Å / Cor.coef. Fo:Fc: 0.9431 / Cor.coef. Fo:Fc free: 0.9085 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.122 / SU Rfree Cruickshank DPI: 0.123
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Displacement parameters | Biso mean: 16.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.81→48.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.94 Å / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Details: chain A / Origin x: 15.2374 Å / Origin y: 0.4343 Å / Origin z: 11.3567 Å
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Refinement TLS group | Selection details: { A|* } |