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- PDB-3g1w: Crystal structure of sugar ABC transporter (sugar-binding protein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g1w | ||||||
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Title | Crystal structure of sugar ABC transporter (sugar-binding protein) from Bacillus halodurans | ||||||
![]() | Sugar ABC transporter | ||||||
![]() | TRANSPORT PROTEIN / Sugar ABC transporter / Sugar-binding protein / Bacillus halodurans / target 11229f / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Sugar ABC transporter (Sugar-binding protein)![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Z. / Eswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: The crystal structure of sugar ABC transporter (sugar-binding protein) from Bacillus halodurans. Authors: Zhang, Z. / Eswaramoorthy, S. / Swaminathan, S. / Burley, S.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122 KB | Display | ![]() |
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PDB format | ![]() | 101.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33860.379 Da / Num. of mol.: 2 / Fragment: UNP residues 42-333 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS pH 6.5, 30% v/v PEG 550, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2009 / Details: mirrors |
Radiation | Monochromator: Si(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→50 Å / Num. all: 33281 / Num. obs: 33281 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.02→2.05 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.1 / % possible all: 88.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines. Program Phenix.refine has also been used in refinement.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→33.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.08 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 34.321 Å / Origin y: 42.02 Å / Origin z: 54.056 Å
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Refinement TLS group |
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