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Open data
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Basic information
Entry | Database: PDB / ID: 1toa | ||||||
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Title | PERIPLASMIC ZINC BINDING PROTEIN TROA FROM TREPONEMA PALLIDUM | ||||||
![]() | PROTEIN (PERIPLASMIC BINDING PROTEIN TROA) | ||||||
![]() | BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / ZINC BINDING PROTEIN / ABC TRANSPORTER | ||||||
Function / homology | ![]() zinc ion transport / periplasmic space / cell adhesion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lee, Y.H. / Deka, R.K. / Norgard, M.V. / Radolf, J.D. / Hasemann, C.A. | ||||||
![]() | ![]() Title: Treponema pallidum TroA is a periplasmic zinc-binding protein with a helical backbone. Authors: Lee, Y.H. / Deka, R.K. / Norgard, M.V. / Radolf, J.D. / Hasemann, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.4 KB | Display | ![]() |
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PDB format | ![]() | 98.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 452.8 KB | Display | |
Data in XML | ![]() | 26.8 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.457452, 0.889145, 0.012599), Vector: |
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Components
#1: Protein | Mass: 34465.883 Da / Num. of mol.: 2 / Fragment: SOLUBLE FRACTION Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH ZINC / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | N-TERM 27 AAS OF PROTEIN DERIVE FROM EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC / Detector: CCD / Date: Oct 15, 1998 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 62551 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 3.66 % / Biso Wilson estimate: 22.59 Å2 / Rsym value: 0.043 / Net I/σ(I): 38.9 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.37 % / Mean I/σ(I) obs: 4.25 / Rsym value: 0.28 / % possible all: 99.7 |
Reflection | *PLUS Rmerge(I) obs: 0.043 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.28 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 27.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: ENGH & HUBER / Topol file: ENGH & HUBER | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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