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Yorodumi- PDB-2bvn: E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bvn | ||||||
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Title | E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa | ||||||
Components | ELONGATION FACTOR TU | ||||||
Keywords | ELONGATION FACTOR / TRANSLATION / GTPASE / ANTIBIOTIC / GTP-BINDING / PHOSPHORYLATION | ||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor complex / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Parmeggiani, A. / Krab, I.M. / Watanabe, T. / Nielsen, R.C. / Dahlberg, C. / Nyborg, J. / Nissen, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Enacyloxin Iia Pinpoints a Binding Pocket of Elongation Factor TU for Development of Novel Antibiotics. Authors: Parmeggiani, A. / Krab, I.M. / Watanabe, T. / Nielsen, R.C. / Dahlberg, C. / Nyborg, J. / Nissen, P. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" 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 "BD" 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 SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bvn.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bvn.ent.gz | 128.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bvn_validation.pdf.gz | 601.9 KB | Display | wwPDB validaton report |
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Full document | 2bvn_full_validation.pdf.gz | 626.1 KB | Display | |
Data in XML | 2bvn_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 2bvn_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/2bvn ftp://data.pdbj.org/pub/pdb/validation_reports/bv/2bvn | HTTPS FTP |
-Related structure data
Related structure data | 1ob5C 1ob2S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.50038, -0.8658, 0.0029), Vector: |
-Components
#1: Protein | Mass: 43239.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: BL21 References: UniProt: P0A6N1, UniProt: P0CE48*PLUS, EC: 3.6.1.48 #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.4 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 2 MICROL PROTEIN SOLUTION MIXED WITH 1 MICROL RESERVOIR SOLUTION (450 MM NACL. 22% PEG6000, 6% GLYCEROL, 7 MM MGCL2, 100 MM TRIS-HCL PH 7.5), SITTING DROP 19 DEG. C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9792 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 25, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 37737 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / % possible all: 53.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OB2 Resolution: 2.3→29.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3463299.91 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 33.7032 Å2 / ksol: 0.313266 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.81 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.06 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.35 Å / Total num. of bins used: 15
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