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- PDB-4z6x: The 1.68-angstrom crystal structure of acitive-site metal-free Pq... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4z6x | ||||||
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Title | The 1.68-angstrom crystal structure of acitive-site metal-free PqqB from Pseudomonas putida | ||||||
![]() | Coenzyme PQQ synthesis protein B | ||||||
![]() | HYDROLASE / PqqB / PQQ / Pyrroloquinoline quinone / metallo-beta-lactamase / lactamase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tu, X. / Wilmot, C.M. | ||||||
![]() | ![]() Title: Crystal structures of PqqB reveal metal-binding plasticity at the active site of PqqB Authors: Tu, X. / Wilmot, C.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.5 KB | Display | ![]() |
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PDB format | ![]() | 113.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.5 KB | Display | ![]() |
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Full document | ![]() | 431.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jxpS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 34123.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: KT2440 / Gene: pqqB, PP_0379 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.87 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: PEG4000, NaCl, BisTris |
-Data collection
Diffraction | Mean temperature: 108 K | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.68→28.9 Å / Num. obs: 46746 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 30.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.023 / Net I/σ(I): 18.2 / Num. measured all: 211169 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 4 % / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3JXP Resolution: 1.68→27.896 Å / FOM work R set: 0.9052 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 163.17 Å2 / Biso mean: 43.11 Å2 / Biso min: 17.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.68→27.896 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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