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- PDB-1e5k: CRYSTAL STRUCTURE OF THE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1e5k | ||||||
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Title | CRYSTAL STRUCTURE OF THE MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN MOBA (PROTEIN FA) FROM ESCHERICHIA COLI AT NEAR ATOMIC RESOLUTION | ||||||
![]() | MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN A | ||||||
![]() | MOLYBDOPTERIN NUCLEOTIDYL-TRANSFERASE | ||||||
Function / homology | ![]() molybdenum cofactor guanylyltransferase / molybdenum cofactor guanylyltransferase activity / bis(molybdopterin guanine dinucleotide)molybdenum biosynthetic process / nucleotidyltransferase activity / GTP binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stevenson, C.E.M. / Sargent, F. / Buchanan, G. / Palmer, T. / Lawson, D.M. | ||||||
![]() | ![]() Title: Crystal Structure of the Molybdenum Cofactor Biosynthesis Protein Moba from Escherichia Coli at Near Atomic Resolution Authors: Stevenson, C.E.M. / Sargent, F. / Buchanan, G. / Palmer, T. / Lawson, D.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.7 KB | Display | ![]() |
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PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
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Full document | ![]() | 443.4 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 16.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22585.814 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE WILD-TYPE CONSTRUCT WAS C-TERMINALLY EXTENDED WITH A 7-RESIDUE NICKEL AFFINITY TAG OF SEQUENCE SER-HIS-HIS-HIS-HIS-HIS-HIS. Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-LI / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | FUNCTION: BIOSYNTHESIS OF MOLYBDOPTERIN GUANINE DINUCLEOTIDE. SEEMS TO BE INVOLVED IN THE ...FUNCTION: BIOSYNTHES | Sequence details | C-TERMINAL TAG: SER-HIS-HIS-HIS-HIS-HIS-HIS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 12 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 20% (V/V) ISOPROPANOL, 2% (W/V) PEG 1500, IN 100 MM CITRIC ACID ...Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 12 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 20% (V/V) ISOPROPANOL, 2% (W/V) PEG 1500, IN 100 MM CITRIC ACID BROUGHT TO PH 5.5 WITH NAOH. CRYSTALS GROW AT 4 DEG. C AND TAKE UP TO 8 WEEKS TO REACH FULL SIZE. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM / Detector: CCD / Date: Feb 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40 Å / Num. obs: 38263 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 5.2 / % possible all: 83.4 |
Reflection shell | *PLUS % possible obs: 83.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Details: ANISOTROPIC THERMAL PARAMETER REFINEMENT WAS USED FOR LAST CYCLE. RESIDUES 15 A TO 21 A WERE POORLY DEFINED IN ELECTRON DENSITY MAPS. ALL LARGE SIDE-CHAINS IN THIS REGION WERE TRUNCATED TO ALA.
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Displacement parameters | Biso mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.184 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |