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- PDB-1vpl: Crystal structure of ABC transporter ATP-binding protein (TM0544)... -
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Basic information
Entry | Database: PDB / ID: 1vpl | ||||||
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Title | Crystal structure of ABC transporter ATP-binding protein (TM0544) from Thermotoga maritima at 2.10 A resolution | ||||||
![]() | ABC transporter, ATP-binding protein | ||||||
![]() | LYASE / TM0544 / ABC TRANSPORTER ATP-BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of ABC transporter ATP-binding protein (TM0544) from Thermotoga maritima at 2.10 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 64 KB | Display | ![]() |
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PDB format | ![]() | 46.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ji0S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 28627.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4 Details: 0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2004 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91837 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.23 Å / Num. obs: 20216 / % possible obs: 99.2 % / Redundancy: 8 % / Biso Wilson estimate: 36.34 Å2 / Rsym value: 0.119 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 1371 / Rsym value: 0.66 / % possible all: 92.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1JI0 Resolution: 2.1→39.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.791 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / 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: 31.602 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→39.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 28.0603 Å / Origin y: 34.1259 Å / Origin z: 15.2603 Å
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Refinement TLS group | Selection: ALL |