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Yorodumi- PDB-4pmn: Crystal structure of the Mycobacterium tuberculosis Tat-secreted ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pmn | ||||||
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Title | Crystal structure of the Mycobacterium tuberculosis Tat-secreted protein Rv2525c in complex with MES (monoclinic crystal form I) | ||||||
Components | Tat-secreted protein Rv2525c | ||||||
Keywords | UNKNOWN FUNCTION / Tat secretion GH25 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 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 | 4pmn.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pmn.ent.gz | 145.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pmn_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 4pmn_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 4pmn_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 4pmn_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/4pmn ftp://data.pdbj.org/pub/pdb/validation_reports/pm/4pmn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25573.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: MT2601 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P95028 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2 M Na formate, 100 mM sodium Acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→37.25 Å / Num. all: 68166 / Num. obs: 68164 / % possible obs: 92.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.44→1.47 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.4 / % possible all: 58.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.44→37.25 Å / Cor.coef. Fo:Fc: 0.9544 / Cor.coef. Fo:Fc free: 0.9483 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.062
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Displacement parameters | Biso mean: 16.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.152 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.44→37.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.48 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: { B|31 - B|240 } |