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Yorodumi- PDB-2c4b: Inhibitor cystine knot protein McoEeTI fused to the catalytically... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c4b | ||||||
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Title | Inhibitor cystine knot protein McoEeTI fused to the catalytically inactive barnase mutant H102A | ||||||
Components | BARNASE MCOEETI FUSION | ||||||
Keywords | FUSION PROTEIN / SQUASH INHIBITOR / HYBRID MICROPROTEIN / RIBONUCLEASE / ENDONUCLEASE / HYDROLASE / NUCLEASE / PROTEASE INHIBITOR / SERINE PROTEASE INHIBITOR | ||||||
Function / homology | Function and homology information negative regulation of serine-type endopeptidase activity / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / serine-type endopeptidase inhibitor activity / defense response / RNA binding / extracellular region Similarity search - Function | ||||||
Biological species | BACILLUS AMYLOLIQUEFACIENS (bacteria) MOMORDICA COCHINCHINENSIS (spiny bitter cucumber) ECBALLIUM ELATERIUM (jumping cucumber) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Niemann, H.H. / Schmoldt, H.U. / Wentzel, A. / Kolmar, H. / Heinz, D.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Barnase Fusion as a Tool to Determine the Crystal Structure of the Small Disulfide-Rich Protein Mcoeeti. Authors: Niemann, H.H. / Schmoldt, H.U. / Wentzel, A. / Kolmar, H. / 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 | 2c4b.cif.gz | 167.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c4b.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/2c4b ftp://data.pdbj.org/pub/pdb/validation_reports/c4/2c4b | HTTPS FTP |
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-Related structure data
Related structure data | 1a2pS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15727.701 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MCOEETI IS A HYBRID OF MCOTI-II AND EETI-II. IT WAS FUSED C-TERMINALLY TO THE H102A MUTANT OF BARNASE WITH A 4-RESIDUE LINKER Source: (gene. exp.) BACILLUS AMYLOLIQUEFACIENS (bacteria), (gene. exp.) MOMORDICA COCHINCHINENSIS (spiny bitter cucumber), (gene. exp.) ECBALLIUM ELATERIUM (jumping cucumber) Description: MCOEETI IS A DESIGNED HYBRID CARRYING SEQUENCE DERIVED FROM MOMORDICA COCHINCHINENSIS MCOTI-II AND ECBALLIUM ELATERIUM EETI-II Plasmid: PBAR100 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): 71-18 References: UniProt: P00648, UniProt: P82409, UniProt: P12071, EC: 3.1.27.3 |
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-Non-polymers , 8 types, 560 molecules
#2: Chemical | ChemComp-2PE / #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-UNX / #8: Chemical | ChemComp-MES / | #9: Water | ChemComp-HOH / | |
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-Details
Compound details | HYDROLYZES PHOSPHODIESTER BONDS IN RNA, POLY- AND OLIGORIBONUCLEOTIDES, INHIBITS TRYPSIN ENGINEERED ...HYDROLYZES |
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Sequence details | RESIDUES 111-114:LINKER RESIDUES, 115-130 FROM MCOTI-II (UNIPROT P82409), RESIDUES 127-144 FROM ...RESIDUES 111-114:LINKER RESIDUES, 115-130 FROM MCOTI-II (UNIPROT P82409), RESIDUES 127-144 FROM EETI-II (UNIPROT P12071) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.3 M AMMONIUM SULPHATE, 7% PEG400 (V/V), 0.1 M MES PH 6.5 AS RESERVOIR SOLUTION. DROPLETS MIXED FROM 8 UL PROTEIN (30 MG/ML) AND 4 UL RESERVOIR. SITTING DROP VAPOR DIFFUSION. 4 DEG. C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 19, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→39.8 Å / Num. obs: 114401 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.3→1.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.42 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A2P Resolution: 1.3→39.84 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.44 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→39.84 Å
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Refine LS restraints |
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