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- PDB-2ux6: Pseudoazurin with engineered amicyanin ligand loop, oxidized form... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ux6 | ||||||
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Title | Pseudoazurin with engineered amicyanin ligand loop, oxidized form, pH 7.5 | ||||||
![]() | PSEUDOAZURIN | ||||||
![]() | ELECTRON TRANSPORT / TYPE-1 COPPER / METAL-BINDING / REDOX POTENTIAL / COPPER / TRANSPORT / CUPREDOXIN / PERIPLASMIC / SPECTROSCOPIC PROPERTIES / LOOP SHORTENING / PROTEIN SCAFFOLD / ELECTRON TRANSFER | ||||||
Function / homology | ![]() electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Velarde, M. / Huber, R. / Yanagisawa, S. / Dennison, C. / Messerschmidt, A. | ||||||
![]() | ![]() Title: Influence of Loop Shortening on the Metal Binding Site of Cupredoxin Pseudoazurin. Authors: Velarde, M. / Huber, R. / Yanagisawa, S. / Dennison, C. / Messerschmidt, 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 | ![]() | 41.7 KB | Display | ![]() |
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PDB format | ![]() | 28.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 410.1 KB | Display | ![]() |
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Full document | ![]() | 410.7 KB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ux7C ![]() 2uxfC ![]() 2uxgC ![]() 1bqkS 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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Unit cell |
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Components
#1: Protein | Mass: 12868.755 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE C-TERMINAL LIGAND-BINDING LOOP BETWEEN H81 AND M86 HAS BEEN REPLACED BY THE RESPECTIVE SHORTER LOOP OF AMICYANIN Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CU / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
Sequence details | THIS SEQUENCE CONTAINS THE SIGNAL PEPTIDE SEQUENCE. THE MATURE SEQUENCE STARTS AT A29 AND HAS 124 ...THIS SEQUENCE CONTAINS THE SIGNAL PEPTIDE SEQUENCE. THE MATURE SEQUENCE STARTS AT A29 AND HAS 124 AMINO ACID REDIDUES. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.16 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP VAPOR DIFFUSION METHOD, MIXING 1MICRO-L OF PROTEIN (20 MG/ML IN 50 MM TRIS/HCL, PH 7.5 PLUS 30 MM NACL) WITH 1 MICRO-L RESERVOIR SOLUTION (10 MM TRIS/HCL, PH 7.5 PLUS 2 M ...Details: HANGING DROP VAPOR DIFFUSION METHOD, MIXING 1MICRO-L OF PROTEIN (20 MG/ML IN 50 MM TRIS/HCL, PH 7.5 PLUS 30 MM NACL) WITH 1 MICRO-L RESERVOIR SOLUTION (10 MM TRIS/HCL, PH 7.5 PLUS 2 M AMMONIUM SULFATE PLUS 2 M NACL). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 21, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 28824 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.1 / % possible all: 71.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BQK Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.995 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP A10 TO A15 HAS BEEN MODELED WITH TWO MAIN CHAIN CONFORMATIONS. SOME SIDE CHAINS HAVE BEEN MODELED WITH TWO ALTERNATE SIDE CHAIN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP A10 TO A15 HAS BEEN MODELED WITH TWO MAIN CHAIN CONFORMATIONS. SOME SIDE CHAINS HAVE BEEN MODELED WITH TWO ALTERNATE SIDE CHAIN CONFORMATIONS. THE COPPER AND SULFUR ATOMS HAVE BEEN REFINED ANISOTROPICALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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