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- PDB-1aw1: TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS COMPLEXED WITH 2-PHOS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1aw1 | ||||||
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Title | TRIOSEPHOSPHATE ISOMERASE OF VIBRIO MARINUS COMPLEXED WITH 2-PHOSPHOGLYCOLATE | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE | ||||||
![]() | ISOMERASE / PSYCHROPHILIC / VIBRIO MARINUS | ||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Maes, D. / Zeelen, J.P. / Wierenga, R.K. | ||||||
![]() | ![]() Title: Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties. Authors: Alvarez, M. / Zeelen, J.P. / Mainfroid, V. / Rentier-Delrue, F. / Martial, J.A. / Wyns, L. / Wierenga, R.K. / Maes, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 367.8 KB | Display | ![]() |
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PDB format | ![]() | 304.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 485.3 KB | Display | ![]() |
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Full document | ![]() | 518.9 KB | Display | |
Data in XML | ![]() | 74 KB | Display | |
Data in CIF | ![]() | 100.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1aw2C ![]() 1treS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 26766.199 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH 2-PHOSPHOGLYCOLATE / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PGA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 100MM TRIETHANOLAMINE/HCL 2.OM AMMONIUM SULFATE, 1MM DTT, EDTA, NAN3 20MM PGA PH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: DOUBLE FOCUSSING MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→25 Å / Num. obs: 59692 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 7 / % possible all: 98.2 |
Reflection | *PLUS Num. measured all: 332463 |
Reflection shell | *PLUS % possible obs: 98.2 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TRE Resolution: 2.7→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.25 |