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Yorodumi- PDB-4rmm: Crystal Structure of the Q7NVP2_CHRVO protein from Chromobacteriu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rmm | ||||||
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Title | Crystal Structure of the Q7NVP2_CHRVO protein from Chromobacterium violaceum. Northeast Structural Genomics Consortium Target CvR191 | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | UNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Q7NVP2_CHRVO / CvR191 | ||||||
Function / homology | Phenylacetic acid degradation-related domain / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / 4HBT domain-containing protein Function and homology information | ||||||
Biological species | Chromobacterium violaceum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Vorobiev, S. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Q7NVP2_CHRVO protein from Chromobacterium violaceum. Authors: Vorobiev, S. / Su, M. / Seetharaman, J. / Mao, L. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rmm.cif.gz | 64.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rmm.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rmm_validation.pdf.gz | 433.4 KB | Display | wwPDB validaton report |
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Full document | 4rmm_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 4rmm_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 4rmm_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/4rmm ftp://data.pdbj.org/pub/pdb/validation_reports/rm/4rmm | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | IT IS POSSIBLE THAT THE TRIMER OBSERVED IN AGGREGATION SCREENING IS NOT STABLE UNDER CRYSTALLIZATION CONDITIONS. |
-Components
#1: Protein | Mass: 18013.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium violaceum (bacteria) Strain: ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757 Gene: CV_2300 / Plasmid: CvR191-21.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q7NVP2 |
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#2: 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: 1.86 Å3/Da / Density % sol: 33.77 % |
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Crystal grow | Temperature: 291 K / Method: microbatch under parafin oil / pH: 7 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization solution: 20% PEG 4000, 0.1M potassium nitrate, 0.1M Bis-Tris propane, pH 7.0, microbatch under ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization solution: 20% PEG 4000, 0.1M potassium nitrate, 0.1M Bis-Tris propane, pH 7.0, microbatch under parafin oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 13220 / Num. obs: 13206 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 50.11 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 36.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 2.07 / Num. unique all: 1313 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→43.855 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 31.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 184.6 Å2 / Biso mean: 85.715 Å2 / Biso min: 31.44 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43.855 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: 39.0368 Å / Origin y: 28.8089 Å / Origin z: 51.9182 Å
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Refinement TLS group | Selection details: chain A |