+Open data
-Basic information
Entry | Database: PDB / ID: 1h6t | ||||||
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Title | Internalin B: crystal structure of fused N-terminal domains. | ||||||
Components | INTERNALIN B | ||||||
Keywords | CELL ADHESION / LEUCINE RICH REPEAT / IG-LIKE DOMAIN / EF-HAND DOMAIN | ||||||
Function / homology | Function and homology information peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | LISTERIA MONOCYTOGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 1h6t.cif.gz | 80.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h6t.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 1h6t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h6t_validation.pdf.gz | 364.4 KB | Display | wwPDB validaton report |
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Full document | 1h6t_full_validation.pdf.gz | 367 KB | Display | |
Data in XML | 1h6t_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1h6t_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h6t ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h6t | HTTPS FTP |
-Related structure data
Related structure data | 1h6uC 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: 32395.943 Da / Num. of mol.: 1 / Fragment: LRR DOMAIN, RESIDUES 36-321 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: P25147, UniProt: P0DQD2*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | THE FIVE N-TERMINAL RESIDUES (GLY PRO LEU GLY SER)WERE INTRODUCED AS PART OF THE CLONING STRATEGY ...THE FIVE N-TERMINAL RESIDUES (GLY PRO LEU 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: 0.2M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 5.0, 13% W/V PEG 4000, 6% V/V 2-METHYL-2,4-PENTANDIOL, T=20C, PROTEIN CONC.=10 MG/ML | |||||||||||||||||||||||||
Crystal grow | *PLUS 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 AFC-5 / Wavelength: 1.5418 |
Detector | Type: RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 10, 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 Lowest resolution: 40 Å / Num. obs: 67222 / % possible obs: 93.2 % |
Reflection shell | *PLUS % possible obs: 88.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D0B Resolution: 1.6→62 Å / SU B: 2.22 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.11
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Refinement step | Cycle: LAST / Resolution: 1.6→62 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.182 / Rfactor Rfree: 0.229 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |