- PDB-5aq6: Structure of E. coli ZinT at 1.79 Angstrom -
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Basic information
Entry
Database: PDB / ID: 5aq6
Title
Structure of E. coli ZinT at 1.79 Angstrom
Components
METAL-BINDING PROTEIN ZINT
Keywords
METAL BINDING PROTEIN / ZINC TRANSPORT / NATURAL HIS-TAG / METAL RESISTANCE
Function / homology
Function and homology information
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
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 2.1 Å / Relative weight: 1
Reflection
Resolution: 1.79→45.8 Å / Num. obs: 28379 / % possible obs: 99.6 % / Observed criterion σ(I): 1.7 / Redundancy: 6.7 % / Biso Wilson estimate: 24.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.6
Reflection shell
Resolution: 1.79→1.85 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 97
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
PROGRAMPACKAGE
datareduction
XDS
PROGRAMPACKAGE
datascaling
HKL2Map
phasing
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 1.79→47.754 Å / SU ML: 0.17 / σ(F): 1.84 / Phase error: 20.66 / Stereochemistry target values: ML Details: THE CLOSE CONTACTS BETWEEN THE ATOMS ZN1, ZN2, ZN3, ZN4, ZN6 AND ZN8 AND THE RESPECTIVE SIDE CHAINS ARE DUE TO COORDINATION DISTANCES.
Rfactor
Num. reflection
% reflection
Rfree
0.2083
1433
5.1 %
Rwork
0.1746
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-
obs
0.1763
28294
99.55 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.79→47.754 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1541
0
12
179
1732
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.012
1642
X-RAY DIFFRACTION
f_angle_d
1.318
2227
X-RAY DIFFRACTION
f_dihedral_angle_d
15.056
604
X-RAY DIFFRACTION
f_chiral_restr
0.051
222
X-RAY DIFFRACTION
f_plane_restr
0.006
292
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7901-1.854
0.3262
141
0.2679
2536
X-RAY DIFFRACTION
97
1.854-1.9283
0.256
135
0.2359
2649
X-RAY DIFFRACTION
100
1.9283-2.016
0.245
131
0.1948
2633
X-RAY DIFFRACTION
100
2.016-2.1223
0.2193
136
0.1842
2649
X-RAY DIFFRACTION
100
2.1223-2.2553
0.2309
152
0.1839
2652
X-RAY DIFFRACTION
100
2.2553-2.4294
0.2245
152
0.1728
2673
X-RAY DIFFRACTION
100
2.4294-2.6739
0.2103
144
0.1661
2684
X-RAY DIFFRACTION
100
2.6739-3.0607
0.1829
150
0.17
2703
X-RAY DIFFRACTION
100
3.0607-3.8559
0.1989
148
0.1575
2762
X-RAY DIFFRACTION
100
3.8559-47.7713
0.1869
144
0.1679
2920
X-RAY DIFFRACTION
100
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.0348
-0.2394
0.0997
0.7668
0.0106
0.4422
0.0837
0.3023
-0.1362
-0.1114
-0.1836
-0.0476
0.2344
0.1932
-0.042
0.1828
0.0494
-0.0031
0.2248
0.0019
0.188
56.9463
16.2579
22.0887
2
1.5322
0.1597
0.2093
1.7185
-0.4845
0.8088
0.1366
-0.0074
0.0929
0.4002
-0.3471
-0.1865
-0.4807
0.8713
-0.133
0.1331
-0.0944
-0.0988
0.5428
0.0714
0.2137
71.4552
20.3184
40.7578
3
0.6274
-0.2438
-0.4731
0.7434
-0.2033
0.9956
-0.1156
-0.1314
0.1802
0.1544
-0.0214
0.0718
-0.4815
0.335
-0.1397
0.2624
-0.1074
-0.0541
0.2671
0.0188
0.201
59.7385
26.0317
37.5371
4
0.1293
-0.1843
0.004
0.238
0.1125
0.4734
-0.0853
-0.3918
0.0843
0.3271
0.2086
-0.0216
-0.4777
-0.4951
0.0043
0.3731
0.0771
-0.0001
0.2185
-0.0268
0.2802
44.5418
29.8828
37.4893
5
0.1989
-0.3296
-0.0413
0.5943
0.1669
0.6406
0.1784
0.24
0.1302
-0.1136
-0.3092
-0.0456
-0.6203
0.2056
-0.1159
0.2556
-0.0045
0.0157
0.2751
0.0808
0.252
52.1569
30.9298
22.784
6
1.7488
-0.7616
0.4091
0.4536
0.2238
1.3965
0.057
0.1002
0.108
-0.0344
-0.115
-0.1564
-0.1108
0.3994
0.0004
0.2013
-0.0569
-0.0155
0.1926
0.0246
0.2005
57.6345
22.9003
30.7929
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAIN 'A' AND (RESID28THROUGH65 )
2
X-RAY DIFFRACTION
2
CHAIN 'A' AND (RESID66THROUGH89 )
3
X-RAY DIFFRACTION
3
CHAIN 'A' AND (RESID90THROUGH113 )
4
X-RAY DIFFRACTION
4
CHAIN 'A' AND (RESID114THROUGH127 )
5
X-RAY DIFFRACTION
5
CHAIN 'A' AND (RESID128THROUGH160 )
6
X-RAY DIFFRACTION
6
CHAIN 'A' AND (RESID161THROUGH216 )
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