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Open data
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Basic information
Entry | Database: PDB / ID: 1m15 | ||||||
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Title | Transition state structure of arginine kinase | ||||||
![]() | arginine kinase | ||||||
![]() | TRANSFERASE / ARGININE KINASE / CREATINE KINASE / PHOSPHAGEN KINASE / TRANSITION STATE ANALOG / ADENOSINE TRIPHOSPHATE | ||||||
Function / homology | ![]() arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / extracellular space / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yousef, M.S. / Fabiola, F. / Gattis, J.L. / Somasundaram, T. / Chapman, M.S. | ||||||
![]() | ![]() Title: Refinement of the arginine kinase transition-state analogue complex at 1.2 A resolution: mechanistic insights. Authors: Yousef, M.S. / Fabiola, F. / Gattis, J.L. / Somasundaram, T. / Chapman, M.S. #1: ![]() Title: Critical Initial Real-Space Refinement in the Structure Determination of Arginine Kinase Authors: Zhou, G. / Somasundaram, T. / Blanc, E. / Chen, Z. / Chapman, M.S. #2: ![]() Title: Expression, Purification from Inclusion Bodies, and Crystal Characterization of a Transition State Analog Complex of Arginine Kinase: A Model for Studying Phosphagen Kinases Authors: Zhou, G. / Parthasarathy, G. / Somasundaram, T. / Ables, A. / Roy, L. / Strong, S.J. / Ellington, W.R. / Chapman, M.S. #3: ![]() Title: Transition State Structure of Arginine Kinase: Implications for Catalysis of Bimolecular Reactions Authors: Zhou, G. / Somasundaram, T. / Blanc, E. / Parthasarathy, G. / Ellington, W.R. / Chapman, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.9 KB | Display | ![]() |
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PDB format | ![]() | 143.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 856.2 KB | Display | ![]() |
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Full document | ![]() | 860.1 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bgoS S: Starting model for refinement |
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Similar structure data |
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Links
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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: 40249.758 Da / Num. of mol.: 1 / Mutation: E103Q, D112G, G116A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET22b / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 562 molecules 








#2: Chemical | |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ARG / |
#5: Chemical | ChemComp-ADP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 46.36 % |
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Crystal grow | pH: 8 / Details: pH 8 |
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Zhou, G., (1997) Protein Sci., 6, 444. |
Components of the solutions | *PLUS Conc.: 15-20 % / Common name: PEG6000 / Details: pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 1999 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. obs: 115910 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Rsym value: 0.048 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.2→1.23 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.323 / % possible all: 71.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 1112071 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS Highest resolution: 1.2 Å / % possible obs: 71.5 % / Rmerge(I) obs: 0.323 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BGO Resolution: 1.2→6 Å / Num. parameters: 31135 / Num. restraintsaints: 37290 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 4%
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Refine analyze | Num. disordered residues: 8 / Occupancy sum hydrogen: 2820 / Occupancy sum non hydrogen: 3422 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 6 Å / Num. reflection Rfree: 3074 / Rfactor Rfree: 0.1225 / Rfactor Rwork: 0.1082 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 1.24 Å / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.214 |