- PDB-3in2: Crystal structure of the N47S/M121L variant of Pseudomonas aerugi... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3in2
Title
Crystal structure of the N47S/M121L variant of Pseudomonas aeruginosa azurin in the Cu(II) state
Components
Azurin
Keywords
ELECTRON TRANSPORT / CUPREDOXIN / AZURIN / GREEK KEY / BETA BARREL / ELECTRON TRANSFER / Copper / Disulfide bond / Metal-binding / Periplasm / Transport
Function / homology
Function and homology information
transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding Similarity search - Function
Azurin / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology
Type: ADSC QUANTUM 315 / Detector: CCD Details: Cryogenically cooled double crystal monochromator with horizontally focusing sagitally bent second mono crystal
Radiation
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.1 Å / Relative weight: 1
Reflection
Resolution: 2.6→50 Å / Num. obs: 4005 / % possible obs: 92.8 % / Redundancy: 22.2 % / Net I/σ(I): 26.5
Reflection shell
Resolution: 2.6→2.7 Å
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Processing
Software
Name
Version
Classification
ADSC
Quantum
datacollection
SHELXD
phasing
SHELXL-97
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: AB INITIO / Resolution: 2.6→10 Å / Num. parameters: 3270 / Num. restraintsaints: 4062 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2661
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5 %
RANDOM
Rwork
0.2381
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all
0.2384
4005
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obs
0.2381
3739
92.8 %
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Refine analyze
Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1057
Refinement step
Cycle: LAST / Resolution: 2.6→10 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
971
0
1
84
1056
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
s_bond_d
0.004
X-RAY DIFFRACTION
s_angle_d
1.56
X-RAY DIFFRACTION
s_similar_dist
0
X-RAY DIFFRACTION
s_from_restr_planes
0.0182
X-RAY DIFFRACTION
s_zero_chiral_vol
0.015
X-RAY DIFFRACTION
s_non_zero_chiral_vol
0.025
X-RAY DIFFRACTION
s_anti_bump_dis_restr
0.005
X-RAY DIFFRACTION
s_rigid_bond_adp_cmpnt
0
X-RAY DIFFRACTION
s_similar_adp_cmpnt
0.091
X-RAY DIFFRACTION
s_approx_iso_adps
0
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