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Yorodumi- PDB-3gmg: Crystal structure of an uncharacterized conserved protein from My... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gmg | ||||||
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Title | Crystal structure of an uncharacterized conserved protein from Mycobacterium tuberculosis | ||||||
Components | Uncharacterized protein Rv1825/MT1873 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cell membrane / Membrane / Transmembrane / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Bonanno, J.B. / Rutter, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of an uncharacterized conserved protein from Mycobacterium tuberculosis Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gmg.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gmg.ent.gz | 51.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gmg_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 3gmg_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 3gmg_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 3gmg_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gmg ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gmg | 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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Details | AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE. |
-Components
#1: Protein | Mass: 17633.984 Da / Num. of mol.: 2 / Fragment: UNP residues 134-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1825, MT1873, MTCY1A11.18c / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P64895, UniProt: P9WFG3*PLUS #2: 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: 2.19 Å3/Da / Density % sol: 43.89 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 6.5 Details: 100mM Bis-Tris pH 6.5, 25% PEG 3350, 200mM Sodium chloride, VAPOR DIFFUSION, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 13, 2009 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→51.723 Å / Num. all: 50353 / Num. obs: 50353 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 25.2 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 7.8 / Num. unique all: 7254 / Rsym value: 0.289 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→18 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.19 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.886 / SU B: 1.035 / SU ML: 0.04 / SU R Cruickshank DPI: 0.069 / SU Rfree: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.93 Å2 / Biso mean: 18.623 Å2 / Biso min: 8.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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