+Open data
-Basic information
Entry | Database: PDB / ID: 1np6 | ||||||
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Title | Crystal structure of Escherichia coli MobB | ||||||
Components | Molybdopterin-guanine dinucleotide biosynthesis protein B | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Mixed alpha-beta fold / elongated beta-sheet / Walker A motif / P-loop structural motif | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | McLuskey, K. / Harrison, J.A. / Schuttelkopf, A.W. / Boxer, D.H. / Hunter, W.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Insight into the role of Escherichia coli MobB in Molybdenum cofactor biosynthesis based on the high resolution crystal structure Authors: McLuskey, K. / Harrison, J.A. / Schuttelkopf, A.W. / Boxer, D.H. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1np6.cif.gz | 80.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1np6.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 1np6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1np6_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 1np6_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 1np6_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1np6_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1np6 ftp://data.pdbj.org/pub/pdb/validation_reports/np/1np6 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The asymmetic unit contains the biological assembly which is a homodimer. |
-Components
#1: Protein | Mass: 19258.178 Da / Num. of mol.: 2 / Fragment: Subunit A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MOBB OR B3856 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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 | Density Matthews: 2.36 Å3/Da / Density % sol: 47.37 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, ammonium sulphate, glycerol, magnesium chloride, GDP, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2001 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 29445 / Num. obs: 29445 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.9 Å2 / Rsym value: 0.042 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.87→1.94 Å / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2844 / Rsym value: 0.273 / % possible all: 97.5 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 99.3 % / Num. measured all: 364026 / Rmerge(I) obs: 0.042 |
Reflection shell | *PLUS % possible obs: 97.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Partial model of MobB previously solved by MAD Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Shrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.729 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.215 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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