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Yorodumi- PDB-4pmo: Crystal structure of the Mycobacterium tuberculosis Tat-secreted ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pmo | ||||||
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Title | Crystal structure of the Mycobacterium tuberculosis Tat-secreted protein Rv2525c, 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 / MOLECULAR REPLACEMENT / Resolution: 1.33 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 | 4pmo.cif.gz | 182.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pmo.ent.gz | 143 KB | Display | PDB format |
PDBx/mmJSON format | 4pmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pmo_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 4pmo_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 4pmo_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 4pmo_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/4pmo ftp://data.pdbj.org/pub/pdb/validation_reports/pm/4pmo | HTTPS FTP |
-Related structure data
Related structure data | 4pmnSC 4pmqC 4pmrC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 30 - 240 / Label seq-ID: 24 - 234
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-Components
#1: Protein | Mass: 25479.346 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 / Plasmid: pDEST17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P95028 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-NA / #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: 2.02 Å3/Da / Density % sol: 39.21 % |
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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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→37.61 Å / Num. obs: 90524 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.8 / % possible all: 75.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PMN Resolution: 1.33→36.95 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.872 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.776 Å2
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Refinement step | Cycle: 1 / Resolution: 1.33→36.95 Å
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Refine LS restraints |
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