[English] 日本語
Yorodumi- PDB-3gvz: Crystal structure of the protein CV2077 from Chromobacterium viol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gvz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the protein CV2077 from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR62 | ||||||
Components | Uncharacterized protein CV2077 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Peptidase C45 / Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / 4-Layer Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Chromobacterium violaceum ATCC 12472 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Forouhar, F. / Neely, H. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Maglaqui, M. / Owens, L. / Chen, C.X. / Everett, J.K. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Maglaqui, M. / Owens, L. / Chen, C.X. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Protein CV2077 from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR62. Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Maglaqui, M. / Owens, L. / Chen, C.X. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G. ...Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Fang, F. / Xiao, R. / Cunningham, K. / Maglaqui, M. / Owens, L. / Chen, C.X. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gvz.cif.gz | 106.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gvz.ent.gz | 85.9 KB | Display | PDB format |
PDBx/mmJSON format | 3gvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gvz ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gvz | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32776.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum ATCC 12472 (bacteria) Strain: DSM 30191 / IFO 12614 / JCM 1249 / NCIB 9131 / Gene: CV_2077 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7NWB3 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 61.99 % |
---|---|
Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 6.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl pH 7.5. Reservoir solution: 0.1M MES pH 6.5, 20% PEG 10000, MICROBATCH UNDER OIL, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97918 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 7, 2007 / Details: Mirrors |
Radiation | Monochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 40489 / Num. obs: 31015 / % possible obs: 76.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.08 / Net I/σ(I): 13.69 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.16 / Rsym value: 0.155 / % possible all: 52.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.8→19.62 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 216276.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: Program XtalView has also been used in refinement
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 8.82271 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 6.6 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→19.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
|