cellular response to zinc ion starvation / intracellular zinc ion homeostasis / cadmium ion binding / cellular response to cadmium ion / cellular response to hydrogen peroxide / outer membrane-bounded periplasmic space / zinc ion binding / metal ion binding / cytosol Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE SEQUENCE: MAIRLYKLAVALGVFIVSAPAFS THAT IS INCLUDED THE SWISPROT RECORD UPSTREAM OF THE SEQUENCE ...THE SEQUENCE: MAIRLYKLAVALGVFIVSAPAFS THAT IS INCLUDED THE SWISPROT RECORD UPSTREAM OF THE SEQUENCE CRYSTALLISED, CORRESPONDS TO A SIGNAL SEQUENCE THAT IS CLEAVED IN THE MATURE PROTEIN.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal grow
pH: 6.5 Details: 10 MG/ML PROTEIN, 10% PEG 10000, 100 MM SODIUM CACODYLATE, PH = 6.5 20 MM CADMIUM CHLORIDE
Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9664 Å / Relative weight: 1
Reflection
Resolution: 2.1→34.06 Å / Num. obs: 12317 / % possible obs: 93.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.107 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.35
Reflection shell
Resolution: 2.1→2.18 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 3.2 / % possible all: 64.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 34.06 Å
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Processing
Software
Name
Classification
DENZO
datareduction
SCALEPACK
datascaling
AMoRE
phasing
CCP4
phasing
REFMAC
refinement
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: ZN CRYSTAL FORM OF YODA Resolution: 2.1→53.45 Å / SU B: 4.445 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.171 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE FIRST 8 RESIDUES AT THE N-TERMINUS ARE DISORDERED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.208
588
5 %
RANDOM
Rwork
0.169
-
-
-
obs
0.1709
11715
96.17 %
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Displacement parameters
Biso mean: 20.692 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.04 Å2
0 Å2
-0.28 Å2
2-
-
1.1 Å2
0 Å2
3-
-
-
-1.16 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→53.45 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1513
0
4
173
1690
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
bond_d
0.015
X-RAY DIFFRACTION
angle_d
X-RAY DIFFRACTION
angle_deg
1.325
X-RAY DIFFRACTION
plane_restr
0.006
+
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