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Yorodumi- PDB-3zeb: A complex of GlpG with isocoumarin inhibitor covalently bonded to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zeb | ||||||
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Title | A complex of GlpG with isocoumarin inhibitor covalently bonded to serine 201 and histidine 150 | ||||||
Components | RHOMBOID PROTEASE GLPG | ||||||
Keywords | HYDROLASE / INTRA-MEMBRANE PROTEASE / SERINE PROTEASE / ACYL ENZYME | ||||||
Function / homology | Function and homology information rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Vinothkumar, K.R. / voskya, O. / Kuettler, E.V. / Brouwer, A.J. / Liskamp, R.M.J. / Verhelst, S.H.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Activity-Based Probes for Rhomboid Proteases Discovered in a Mass Spectrometry-Based Assay. Authors: Vosyka, O. / Vinothkumar, K.R. / Wolf, E.V. / Brouwer, A.J. / Liskamp, R.M.J. / Verhelst, S.H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zeb.cif.gz | 53.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zeb.ent.gz | 37 KB | Display | PDB format |
PDBx/mmJSON format | 3zeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/3zeb ftp://data.pdbj.org/pub/pdb/validation_reports/ze/3zeb | HTTPS FTP |
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-Related structure data
Related structure data | 2xovS 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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Unit cell |
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-Components
#1: Protein | Mass: 20214.020 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 92-270 Source method: isolated from a genetically manipulated source Details: THE ISOCOUMARIN RING IS OPENED BY THE NUCLEOPHILIC ATTACK OF S201 FORMS ESTER BOND AND SUBSEQUENTLY A REACTION BETWEEN HISTIDINE CREATES A SECOND COVALENT BOND. Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P09391, rhomboid protease | ||||
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#2: Chemical | ChemComp-SV1 / | ||||
#3: Chemical | ChemComp-CL / | ||||
#4: Sugar | ChemComp-BNG / #5: Water | ChemComp-HOH / | Nonpolymer details | 2-PHENYLETHYL 2-(4-AZANYL-2-METHANOYL-PHENYL)ETHANOATE (SV1): THE NUCLEOPHILIC ATTACK OF SER 201 ON ...2-PHENYLETHY | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.8 % / Description: NONE |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2M AMMONIUM CHLORIDE, 0.1 M BIS-TRIS PH7.0, 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.95 Å / Num. obs: 15318 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.1 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XOV Resolution: 2.2→44.99 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.099 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 60 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→44.99 Å
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Refine LS restraints |
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