+Open data
-Basic information
Entry | Database: PDB / ID: 1frw | ||||||
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Title | STRUCTURE OF E. COLI MOBA WITH BOUND GTP AND MANGANESE | ||||||
Components | MOLYBDOPTERIN-GUANINE DINUCLEOTIDE BIOSYNTHESIS PROTEIN | ||||||
Keywords | METAL BINDING PROTEIN / Molybdenum cofactor (Moco) / Moco Biosynthesis / Molybdopterin (MPT) / Molybdopterin Guanine Dinucleotide (MGD) | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.75 Å | ||||||
Authors | Lake, M.W. / Temple, C.A. / Rajagopalan, K.V. / Schindelin, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: The crystal structure of the Escherichia coli MobA protein provides insight into molybdopterin guanine dinucleotide biosynthesis. Authors: Lake, M.W. / Temple, C.A. / Rajagopalan, K.V. / Schindelin, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1frw.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1frw.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 1frw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1frw_validation.pdf.gz | 815.6 KB | Display | wwPDB validaton report |
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Full document | 1frw_full_validation.pdf.gz | 819.9 KB | Display | |
Data in XML | 1frw_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 1frw_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/1frw ftp://data.pdbj.org/pub/pdb/validation_reports/fr/1frw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is an octamer constructed from chain A. The octamer has 42 symmetry and is entirely generated by crystallographic symmetry operations in the I422 tetragonal space group. His 49 from 2 different monomers along with 2 acetate ligands coordinate a zinc atom at the dimer interface. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21669.854 Da / Num. of mol.: 1 / Fragment: MOBA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PCT800A / Production host: Escherichia coli (E. coli) / References: UniProt: P32173 |
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-Non-polymers , 5 types, 172 molecules
#2: Chemical | ChemComp-ACT / |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-GTP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.08 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium acetate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 26350 / Num. obs: 26350 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.75→1.83 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.441 / Num. unique all: 2895 / % possible all: 100 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Refmac dictionary / Details: Hydrogens have been added in the riding positions
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Solvent computation | Solvent model: Babinet's principle | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |