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Yorodumi- PDB-2wok: Clavulanic acid biosynthesis oligopeptide binding protein 2 compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wok | ||||||
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Title | Clavulanic acid biosynthesis oligopeptide binding protein 2 complexed with bradykinin | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN/PEPTIDE / PEPTIDE BINDING PROTEIN-PEPTIDE COMPLEX / SOLUTE-BINDING PROTEIN / CLAVULANIC ACID BIOSYNTHESIS / OLIGOPEPTIDE BINDING PROTEIN / OLIGOPEPTIDE / BRADYKININ | ||||||
Function / homology | Function and homology information clavulanic acid biosynthetic process / peptide transport / negative regulation of cell adhesion / negative regulation of blood coagulation / peptide transmembrane transporter activity / cysteine-type endopeptidase inhibitor activity / Intrinsic Pathway of Fibrin Clot Formation / ATP-binding cassette (ABC) transporter complex / Peptide ligand-binding receptors / platelet alpha granule lumen ...clavulanic acid biosynthetic process / peptide transport / negative regulation of cell adhesion / negative regulation of blood coagulation / peptide transmembrane transporter activity / cysteine-type endopeptidase inhibitor activity / Intrinsic Pathway of Fibrin Clot Formation / ATP-binding cassette (ABC) transporter complex / Peptide ligand-binding receptors / platelet alpha granule lumen / negative regulation of proteolysis / Post-translational protein phosphorylation / hormone activity / vasodilation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / heparin binding / outer membrane-bounded periplasmic space / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / signaling receptor binding / extracellular space / extracellular exosome / zinc ion binding / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Streptomyces clavuligerus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Mackenzie, A.K. / Valegard, K. / Iqbal, A. / Caines, M.E.C. / Kershaw, N.J. / Jensen, S.E. / Schofield, C.J. / Andersson, I. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2010 Title: Crystal structures of an oligopeptide-binding protein from the biosynthetic pathway of the beta-lactamase inhibitor clavulanic acid. Authors: Mackenzie, A.K. / Valegard, K. / Iqbal, A. / Caines, M.E. / Kershaw, N.J. / Jensen, S.E. / Schofield, C.J. / Andersson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wok.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wok.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wok ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wok | HTTPS FTP |
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-Related structure data
Related structure data | 2wolSC 2wopC 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: 62065.559 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KRB4 | ||
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#2: Protein/peptide | Mass: 1062.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01042 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 8 / Details: pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 10, 2007 / Details: M |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→62.1 Å / Num. obs: 59885 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WOL Resolution: 1.7→62.14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.322 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.119 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→62.14 Å
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