+Open data
-Basic information
Entry | Database: PDB / ID: 1h6u | ||||||
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Title | Internalin H: crystal structure of fused N-terminal domains. | ||||||
Components | INTERNALIN H | ||||||
Keywords | CELL ADHESION / LEUCINE RICH REPEAT / IG-LIKE DOMAIN / EF-HAND DOMAIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LISTERIA MONOCYTOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Schubert, W.-D. / Gobel, G. / Diepholz, M. / Darji, A. / Kloer, D. / Hain, T. / Chakraborty, T. / Wehland, J. / Domann, E. / Heinz, D.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Internalins from the human pathogen Listeria monocytogenes combine three distinct folds into a contiguous internalin domain. Authors: Schubert, W.D. / Gobel, G. / Diepholz, M. / Darji, A. / Kloer, D. / Hain, T. / Chakraborty, T. / Wehland, J. / Domann, E. / Heinz, D.W. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Internalins from the Human Pathogen Listeria Monocytogenes Combine Three Distinct Folds Into a Contiguous Internalin Domain Authors: Schubert, W.-D. / Gobel, G. / Diepholz, M. / Darji, A. / Kloer, D. / Hain, T. / Chakraborty, T. / Wehland, J. / Domann, E. / Heinz, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h6u.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h6u.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 1h6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h6u ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h6u | HTTPS FTP |
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-Related structure data
Related structure data | 1h6tC 1d0bS 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
#1: Protein | Mass: 32585.611 Da / Num. of mol.: 1 / Fragment: LRR DOMAIN, RESIDUES 36-343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LISTERIA MONOCYTOGENES (bacteria) / Strain: EGD (SEROVAR 1/2A) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9ZEY1 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE TWO N-TERMINAL RESIDUES (GLY SER) WERE INTRODUCED AS PART OF THE CLONING STRATEGY (PRESCISSION ...THE TWO N-TERMINAL RESIDUES (GLY SER) WERE INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 42.8 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 5 Details: 10% PEG 8000, 0.1M TRIS PH 7.0, 0.2 M MGCL2. T=20C, PROTEIN CONC.=10 MG/ML | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: sparse matrix method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 3, 2000 / Details: OSMIC CONFOCAL MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→61 Å / Num. obs: 37671 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 7.42 / % possible all: 91.2 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Num. obs: 32149 / % possible obs: 98.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 96.5 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D0B Resolution: 1.8→76.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.536 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.12 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→76.7 Å
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Refine LS restraints |
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