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Yorodumi- PDB-4b4u: Crystal structure of Acinetobacter baumannii N5, N10- methylenete... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b4u | ||||||
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Title | Crystal structure of Acinetobacter baumannii N5, N10- methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD) complexed with NADP cofactor | ||||||
Components | BIFUNCTIONAL PROTEIN FOLD | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / L-histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | ACINETOBACTER BAUMANNII ATCC 19606 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Eadsforth, T.C. / Maluf, F.V. / Hunter, W.N. | ||||||
Citation | Journal: FEBS J. / Year: 2012 Title: Acinetobacter Baumannii Fold Ligand Complexes; Potent Inhibitors of Folate Metabolism and a Re-Evaluation of the Ly374571 Structure. Authors: Eadsforth, T.C. / Maluf, F.V. / 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 | 4b4u.cif.gz | 261.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b4u.ent.gz | 210.5 KB | Display | PDB format |
PDBx/mmJSON format | 4b4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4b4u_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4b4u_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4b4u_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 4b4u_validation.cif.gz | 47.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/4b4u ftp://data.pdbj.org/pub/pdb/validation_reports/b4/4b4u | HTTPS FTP |
-Related structure data
Related structure data | 4b4vC 4b4wC 1b0aS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32146.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACINETOBACTER BAUMANNII ATCC 19606 (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: D0CBC8, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase |
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-Non-polymers , 5 types, 753 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-PEG / | #6: 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: 2.4 Å3/Da / Density % sol: 49.2 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS PH 5.5, 25 % PEG 3350, 0.2M MGCL AND 2 % DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.981 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 25, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.981 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→52.6 Å / Num. obs: 100394 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.9 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B0A Resolution: 1.45→52.6 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.738 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES WITH DISORDERED SIDE CHAINS ARE MODELED WITH AN OCCUPANCY OF 0.00. DISORDERED NICOTINAMIDE AND RIBOSE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.912 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→52.6 Å
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Refine LS restraints |
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