+Open data
-Basic information
Entry | Database: PDB / ID: 1p9n | ||||||
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Title | Crystal structure of Escherichia coli MobB. | ||||||
Components | Molybdopterin-guanine dinucleotide biosynthesis protein B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Molybdopterin cofactor biosynthesis / MobB / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | Function and homology information Mo-molybdopterin cofactor biosynthetic process / GTP binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Rangarajan, S.E. / Tocilj, A. / Li, Y. / Iannuzzi, P. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Molecules of Escherichia coli MobB assemble into densely packed hollow cylinders in a crystal lattice with 75% solvent content. Authors: Rangarajan, S.E. / Tocilj, A. / Li, Y. / Iannuzzi, P. / Matte, A. / Cygler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p9n.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p9n.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 1p9n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p9n_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 1p9n_full_validation.pdf.gz | 475.4 KB | Display | |
Data in XML | 1p9n_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 1p9n_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p9/1p9n ftp://data.pdbj.org/pub/pdb/validation_reports/p9/1p9n | 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
#1: Protein | Mass: 19134.240 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MobB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P32125 #2: Chemical | #3: 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 grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.68 M ammonium sulphate, 50 mM Malonic acid, 15 mM cetyl ammonium bromide, 10 mM MgCl2, 1 mM B-mercaptoethanol., pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97936 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 22, 2002 / Details: NULL |
Radiation | Monochromator: Silicone / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97936 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 40361 / Num. obs: 22303 / % possible obs: 86.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.9 Å2 / Rsym value: 0.183 |
Reflection shell | Resolution: 2.61→2.7 Å / Rsym value: 0.693 / % possible all: 35.5 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 20053 / % possible obs: 98.5 % / Num. measured all: 241509 / Rmerge(I) obs: 0.183 |
Reflection shell | *PLUS % possible obs: 87.5 % / Rmerge(I) obs: 0.716 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→30.92 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.1812 Å2 / ksol: 0.331851 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→30.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 15665 / Num. reflection Rfree: 1545 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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