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Yorodumi- PDB-4b4v: Crystal structure of Acinetobacter baumannii N5, N10- methylenete... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4b4v | ||||||
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Title | Crystal structure of Acinetobacter baumannii N5, N10- methylenetetrahydrofolate dehydrogenase-cyclohydrolase (FolD) complexed with NADP cofactor and inhibitor LY354899 | ||||||
Components | BIFUNCTIONAL PROTEIN FOLD | ||||||
Keywords | OXIDOREDUCTASE / INHIBITOR | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / nucleotide binding Similarity search - Function | ||||||
Biological species | ACINETOBACTER BAUMANNII ATCC 19606 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 | 4b4v.cif.gz | 236.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b4v.ent.gz | 188.6 KB | Display | PDB format |
PDBx/mmJSON format | 4b4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/4b4v ftp://data.pdbj.org/pub/pdb/validation_reports/b4/4b4v | HTTPS FTP |
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-Related structure data
Related structure data | 4b4uC 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, 661 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | NADP NICOTINAMI |
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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: 2.44 Å3/Da / Density % sol: 49.2 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS PH 5.5, 20 % PEG 3350, 0.2 M MGCL2 AND 2 % DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20.67 Å / Num. obs: 36783 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 6.3 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B0A Resolution: 2→20.67 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.07 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES WITH DISORDERED SIDE CHAINS ARE MODELED WITH AN OCCUPANCY OF 0.
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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: 16.728 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20.67 Å
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Refine LS restraints |
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