+Open data
-Basic information
Entry | Database: PDB / ID: 4d56 | ||||||
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Title | Understanding bi-specificity of A-domains | ||||||
Components | APNAA1 | ||||||
Keywords | HYDROLASE / NON-RIBOSOMAL PEPTIDE SYNTHETASE / ADENYLATION / A DOMAIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Planktothrix agardhii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kaljunen, H. / Schiefelbein, S.H.H. / Stummer, D. / Kozak, S. / Meijers, R. / Christiansen, G. / Rentmeister, A. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Structural Elucidation of the Bispecificity of a Domains as a Basis for Activating Non-Natural Amino Acids. Authors: Kaljunen, H. / Schiefelbein, S.H.H. / Stummer, D. / Kozak, S. / Meijers, R. / Christiansen, G. / Rentmeister, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d56.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d56.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 4d56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/4d56 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/4d56 | HTTPS FTP |
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-Related structure data
Related structure data | 4d4gC 4d4hC 4d4iC 4d57C 1amuS 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, 1 molecules A
#1: Protein | Mass: 64590.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Planktothrix agardhii (bacteria) / Strain: PCC7821 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0WVH3 |
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-Non-polymers , 5 types, 168 molecules
#2: Chemical | ChemComp-TYR / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-AMP / | #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: 2 Å3/Da / Density % sol: 37 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 24-30% POLYETHYLENE GLYCOL 3350 0.1 M MES OR BIS-TRIS PH 5.5 - 6. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2006 |
Radiation | Monochromator: DOUBLE CRYSTAL (SI111, SI311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→82.2 Å / Num. obs: 30246 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AMU Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 30.105 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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