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Yorodumi- PDB-5g3y: Crystal structure of adenylate kinase ancestor 1 with Zn and ADP bound -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g3y | ||||||
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Title | Crystal structure of adenylate kinase ancestor 1 with Zn and ADP bound | ||||||
Components | ADENYLATE KINSE | ||||||
Keywords | TRANSFERASE / ADENYLATE KINASE / ADP / PHOSPHORYL TRANSFER / NUCLEOTIDE-BINDING | ||||||
Function / homology | P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ADENOSINE-5'-DIPHOSPHATE Function and homology information | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å | ||||||
Authors | Nguyen, V. / Kutter, S. / English, J. / Kern, D. | ||||||
Citation | Journal: Science / Year: 2017 Title: Evolutionary drivers of thermoadaptation in enzyme catalysis. Authors: Nguyen, V. / Wilson, C. / Hoemberger, M. / Stiller, J.B. / Agafonov, R.V. / Kutter, S. / English, J. / Theobald, D.L. / Kern, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g3y.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g3y.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 5g3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g3y_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5g3y_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5g3y_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 5g3y_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/5g3y ftp://data.pdbj.org/pub/pdb/validation_reports/g3/5g3y | HTTPS FTP |
-Related structure data
Related structure data | 5g3zC 5g40C 5g41C 1p3jS 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
#1: Protein | Mass: 25020.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: adenylate kinase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: 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: 2.09 Å3/Da / Density % sol: 41.29 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.5 UL OF PROTEIN MIXTURE (20 MG/ML ADK ANCESTOR 1 AND 20 MM MGADP IN 40 MM MOPS PH 7.0, 50 MM NACL, 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (100 MM SODIUM ACETATE PH 4.6, 50 MM ...Details: 0.5 UL OF PROTEIN MIXTURE (20 MG/ML ADK ANCESTOR 1 AND 20 MM MGADP IN 40 MM MOPS PH 7.0, 50 MM NACL, 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (100 MM SODIUM ACETATE PH 4.6, 50 MM MGCL2, 2M AMMONIUM SULFATE). CRYSTALS WERE GROWN BY SITTING DROP METHOD AT 18C. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9784 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2014 |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9784 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→47.1 Å / Num. obs: 67513 / % possible obs: 96.7 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.18→1.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P3J Resolution: 1.18→37.7 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.97 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / 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: 15.493 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→37.7 Å
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Refine LS restraints |
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