+Open data
-Basic information
Entry | Database: PDB / ID: 1nks | ||||||
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Title | ADENYLATE KINASE FROM SULFOLOBUS ACIDOCALDARIUS | ||||||
Components | ADENYLATE KINASE | ||||||
Keywords | KINASE / THERMOPHILIC / TRANSFERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.57 Å | ||||||
Authors | Vonrhein, C. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: The structure of a trimeric archaeal adenylate kinase. Authors: Vonrhein, C. / Bonisch, H. / Schafer, G. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nks.cif.gz | 236.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nks.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/1nks ftp://data.pdbj.org/pub/pdb/validation_reports/nk/1nks | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 21137.369 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Plasmid: PET3A / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P35028, adenylate kinase #2: Chemical | #3: Chemical | ChemComp-ADP / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66 % Description: LOW RESOLUTION DATA WERE COLLECTED ON A ROTATING ANODE AND MERGED WITH HIGH-RESOLUTION DATA COLLECTED FROM THE SYNCHROTRON SOURCE DESCRIBED ABOVE. | ||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 2 M SODIUM FORMATE AT PH 7.5 AT A PROTEIN CONCENTRATION OF 5 MG/ML; PROTEIN SOLUTION WAS QUARTZ-DISTILLED AND NO NUCLEOTIDES WERE ADDED. | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9123 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: DUAL SLITS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9123 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→40 Å / Num. obs: 54962 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.091 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.57→2.64 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.266 / % possible all: 56 |
Reflection | *PLUS Num. measured all: 168355 / Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 56 % / Rmerge(I) obs: 0.266 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.57→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT CORRECTION AS IMPLEMENTED IN X-PLOR 3.851 WAS USED.
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Refinement step | Cycle: LAST / Resolution: 2.57→40 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.164 | |||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||
Displacement parameters | *PLUS |