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Yorodumi- PDB-4b2b: Structure of the factor Xa-like trypsin variant triple-Ala (TGPA)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b2b | ||||||
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Title | Structure of the factor Xa-like trypsin variant triple-Ala (TGPA) in complex with eglin C | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information cap snatching / response to wounding / virion component / serine-type endopeptidase inhibitor activity / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | BOS TAURUS (cattle) HIRUDO MEDICINALIS (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å | ||||||
Authors | Menzel, A. / Neumann, P. / Stubbs, M.T. | ||||||
Citation | Journal: Biol.Chem. / Year: 2014 Title: Thermodynamic signatures in macromolecular interactions involving conformational flexibility. Authors: Menzel, A. / Neumann, P. / Schwieger, C. / Stubbs, M.T. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b2b.cif.gz | 249.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b2b.ent.gz | 201.4 KB | Display | PDB format |
PDBx/mmJSON format | 4b2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b2b_validation.pdf.gz | 479.3 KB | Display | wwPDB validaton report |
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Full document | 4b2b_full_validation.pdf.gz | 484.8 KB | Display | |
Data in XML | 4b2b_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 4b2b_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/4b2b ftp://data.pdbj.org/pub/pdb/validation_reports/b2/4b2b | HTTPS FTP |
-Related structure data
Related structure data | 4b1tC 4b2aSC 4b2cC C: citing same article (ref.) 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 oper:
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 23436.414 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00760, trypsin #2: Protein | Mass: 8173.084 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIRUDO MEDICINALIS (medicinal leech) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01051 |
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-Non-polymers , 5 types, 557 molecules
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 38.97 % / Description: NONE |
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Crystal grow | Temperature: 283 K Details: 18% (W/V) PEG 10,000, 20% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 9.0 AND 100 MM NACL AT 283 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 23, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.36→50 Å / Num. obs: 123592 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.36→1.43 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4B2A Resolution: 1.36→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.964 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.057 / 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: 15.922 Å2
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Refinement step | Cycle: LAST / Resolution: 1.36→30 Å
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Refine LS restraints |
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