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Yorodumi- PDB-1r88: The crystal structure of Mycobacterium tuberculosis MPT51 (FbpC1) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r88 | ||||||
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Title | The crystal structure of Mycobacterium tuberculosis MPT51 (FbpC1) | ||||||
Components | MPT51/MPB51 antigen | ||||||
Keywords | IMMUNE SYSTEM / Mycobacterium tuberculosis / alfa/beta hydrolase fold / antigen 85 / MPT51 / FBPC1 | ||||||
Function / homology | Function and homology information mycolate cell wall layer assembly / zymogen binding / acyltransferase activity, transferring groups other than amino-acyl groups / fibronectin binding / extracellular region Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Wilson, R.A. / Maughan, W.N. / Kremer, L. / Besra, G.S. / Futterer, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The structure of Mycobacterium tuberculosis MPT51 (FbpC1) defines a new family of non-catalytic alpha/beta hydrolases. Authors: Wilson, R.A. / Maughan, W.N. / Kremer, L. / Besra, G.S. / Futterer, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r88.cif.gz | 116.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r88.ent.gz | 90.3 KB | Display | PDB format |
PDBx/mmJSON format | 1r88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/1r88 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/1r88 | HTTPS FTP |
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-Related structure data
Related structure data | 1dqzS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 33 - 281 / Label seq-ID: 8 - 256
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Details | The biological assembly is a monomer, represented by either of the two molecules in the asymmetric unit |
-Components
#1: Protein | Mass: 29456.623 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: fbpC1 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P0A4V6, UniProt: P9WQN7*PLUS #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 30, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 78268 / Num. obs: 78268 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.077 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.489 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.7 Å / Num. measured all: 493963 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.489 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1dqz Resolution: 1.71→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.164 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.091 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.208 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3430 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.706→1.798 Å / Total num. of bins used: 10 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å |