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Yorodumi- PDB-2c95: Structure of adenylate kinase 1 in complex with P1,P4-di(adenosin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c95 | ||||||
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Title | Structure of adenylate kinase 1 in complex with P1,P4-di(adenosine) tetraphosphate | ||||||
Components | ADENYLATE KINASE 1 | ||||||
Keywords | TRANSFERASE / AP4A / NUCLEOTIDE KINASE / TRANSFERASE ATP-BINDING | ||||||
Function / homology | Function and homology information nucleoside-triphosphate-adenylate kinase / outer dense fiber / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / (d)CMP kinase activity / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase ...nucleoside-triphosphate-adenylate kinase / outer dense fiber / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / (d)CMP kinase activity / adenylate kinase / adenylate kinase activity / nucleoside-diphosphate kinase / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / ATP metabolic process / phosphorylation / extracellular exosome / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Bunkoczi, G. / Filippakopoulos, P. / Jansson, A. / Longman, E. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Knapp, S. | ||||||
Citation | Journal: To be Published Title: Structure of Adenylate Kinase 1 in Complex with P1, P4-Di(Adenosine)Tetraphosphate Authors: Bunkoczi, G. / Filippakopoulos, P. / Jansson, A. / Longman, E. / von Delft, F. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Weigelt, J. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c95.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c95.ent.gz | 75.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c95_validation.pdf.gz | 993.7 KB | Display | wwPDB validaton report |
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Full document | 2c95_full_validation.pdf.gz | 995.9 KB | Display | |
Data in XML | 2c95_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 2c95_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c95 ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c95 | HTTPS FTP |
-Related structure data
Related structure data | 1z83S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.99992, -0.00611, -0.01096), Vector: |
-Components
#1: Protein | Mass: 21837.957 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PLIC-SGC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00568, adenylate kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE FOR THE PROTEIN BELOW IS FROM A SYNTHETIC CONSTRUCT (GENBANK ID AAQ02450) AND ACCOUNTS ...THE SEQUENCE FOR THE PROTEIN BELOW IS FROM A SYNTHETIC CONSTRUCT (GENBANK ID AAQ02450) AND ACCOUNTS FOR THE SEQUENCE CONFLICTS BELOW. HOWEVER, UNIPROT ENTRY P00568 REMAINS THE CLOSEST MATCH TO THIS SEQUENCE. | |
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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: 2.2 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | pH: 7 / Details: 3.4 M NAMALONATE 1 MM ZNSO4, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 10, 2005 |
Radiation | Monochromator: OSMIC HR MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→32.55 Å / Num. obs: 37771 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.51 |
Reflection shell | Resolution: 1.71→1.81 Å / Redundancy: 0.93 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.06 / % possible all: 41.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z83 Resolution: 1.71→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.249 / SU ML: 0.091 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.13 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 4.87 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→50 Å
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Refine LS restraints |
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