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Yorodumi- PDB-2f6k: Crystal Structure of Amidohydrorolase II; Northeast Structural Ge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f6k | ||||||
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Title | Crystal Structure of Amidohydrorolase II; Northeast Structural Genomics Target LpR24 | ||||||
Components | metal-dependent hydrolase | ||||||
Keywords | LYASE / Metal Dependent Hydrolyse / Aminohydro_2 / ACMDS / ACMS / Tryptophan-NDA metabolism / quinolinic acid / QUIN / nitrobenzoic acid biodegradation / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus plantarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Das, K. / Xiao, R. / Acton, T. / Ma, L. / Arnold, E. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of ACMDS from Lactobacillus plantarum Authors: Das, K. / Xiao, R. / Acton, T. / Ma, L. / Arnold, E. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f6k.cif.gz | 133.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f6k.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 2f6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f6k_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 2f6k_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 2f6k_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 2f6k_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/2f6k ftp://data.pdbj.org/pub/pdb/validation_reports/f6/2f6k | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: -X, Y, -Z+1 |
-Components
#1: Protein | Mass: 34854.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: WCFS1 / Production host: Escherichia coli (E. coli) References: GenBank: 28379401, UniProt: F9US96*PLUS, aminocarboxymuconate-semialdehyde decarboxylase #2: Chemical | #3: 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: 2.95 Å3/Da / Density % sol: 58.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2M Ammonium Sulfate, 0.01M Magnesium Acetate, 0.05M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 27059 / Num. obs: 27059 / % possible obs: 90.5 % / Observed criterion σ(I): -1 / Redundancy: 6 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.7 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→49.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2412968.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.009 Å2 / ksol: 0.319 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→49.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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