[English] 日本語
![](img/lk-miru.gif)
- PDB-1hjj: Biochemical and Structural Analysis of the Molybdenum Cofactor Bi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1hjj | ||||||
---|---|---|---|---|---|---|---|
Title | Biochemical and Structural Analysis of the Molybdenum Cofactor Biosynthesis protein MobA | ||||||
![]() | MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN A | ||||||
![]() | MOLYBDENUM COFACTOR BIOSYNTHESIS / MOLYBDOPTERIN NUCLEOTIDYL-TRANSFERASE / GTP-BINDING | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Guse, A. / Stevenson, C.E.M. / Kuper, J. / Buchanan, G. / Schwarz, G. / Mendel, R.R. / Lawson, D.M. / Palmer, T. | ||||||
![]() | ![]() Title: Biochemical and Structural Analysis of the Molybdenum Cofactor Biosynthesis Protein Moba Authors: Guse, A. / Stevenson, C.E.M. / Kuper, J. / Buchanan, G. / Schwarz, G. / Giordano, G. / Magalon, A. / Mendel, R.R. / Lawson, D.M. / Palmer, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 39.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 1h4cC ![]() 1h4dC ![]() 1h4eC ![]() 1hjlC ![]() 1e5kS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 22586.801 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE FULL LENGTH CONSTRUCT WAS C-TERMINALLY EXTENDED WITH A 7-RESIDUE NICKEL AFFINITY TAG OF SEQUENCE SER-HIS-HIS-HIS-HIS-HIS-HIS. Source: (gene. exp.) ![]() ![]() Description: MUTATION INTRODUCED BY 3-WAY PCR AND VERIFIED BY DNA SEQUENCING Variant: M15[PREP4] / Plasmid: PKK223-3 / Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-LI / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | LINKS A GUANOSINE 5'-PHOSPHATE TO MOLYDOPTERIN (MPT) FORMING MOLYBDOPTERIN GUANINE DINUCLEOTIDE ...LINKS A GUANOSINE 5'-PHOSPHATE TO MOLYDOPTER | Sequence details | N180D MUTANT C-TERMINAL TAG: SER-HIS-HIS-HIS-HIS-HIS-HIS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 / Details: Stevenson, C.E., (2000) Structure, 8, 1115. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. obs: 21218 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.65→1.69 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.9 / % possible all: 88 |
Reflection shell | *PLUS % possible obs: 88 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E5K Resolution: 1.65→54.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.804 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.82 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→54.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|