- PDB-5ere: Extracellular ligand binding receptor from Desulfohalobium retbae... -
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Basic information
Entry
Database: PDB / ID: 5ere
Title
Extracellular ligand binding receptor from Desulfohalobium retbaense DSM5692
Components
Extracellular ligand-binding receptor
Keywords
SIGNALING PROTEIN / Solute Binding Protein / Tandem PAS sensor / ketoleucine / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Leucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I / metal ion binding / ACETIC ACID / 2-OXO-4-METHYLPENTANOIC ACID / 6-AMINOPYRIMIDIN-2(1H)-ONE / Extracellular ligand-binding receptor
Function and homology information
Biological species
Desulfohalobium retbaense DSM 5692 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97918 Å / Relative weight: 1
Reflection
Resolution: 2→50 Å / Num. obs: 53557 / % possible obs: 99.9 % / Redundancy: 20 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 43.1
Reflection shell
Resolution: 2→2.03 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 2.3 / % possible all: 100
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Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
HKL-3000
phasing
HKL-3000
datareduction
Refinement
Method to determine structure: SAD / Resolution: 2→33.187 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.59 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2258
2711
5.08 %
Rwork
0.1721
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obs
0.1748
53415
99.87 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2→33.187 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4069
0
36
223
4328
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.013
4182
X-RAY DIFFRACTION
f_angle_d
1.286
5674
X-RAY DIFFRACTION
f_dihedral_angle_d
15.423
1454
X-RAY DIFFRACTION
f_chiral_restr
0.055
651
X-RAY DIFFRACTION
f_plane_restr
0.006
745
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2-2.0364
0.3651
131
0.3141
2631
X-RAY DIFFRACTION
99
2.0364-2.0755
0.3354
151
0.2679
2594
X-RAY DIFFRACTION
100
2.0755-2.1179
0.2965
150
0.2391
2625
X-RAY DIFFRACTION
100
2.1179-2.1639
0.2403
157
0.2264
2605
X-RAY DIFFRACTION
100
2.1639-2.2143
0.2687
120
0.2027
2663
X-RAY DIFFRACTION
100
2.2143-2.2696
0.2248
160
0.1999
2609
X-RAY DIFFRACTION
100
2.2696-2.331
0.2505
143
0.2031
2642
X-RAY DIFFRACTION
100
2.331-2.3995
0.2265
138
0.1815
2643
X-RAY DIFFRACTION
100
2.3995-2.477
0.2535
143
0.1802
2636
X-RAY DIFFRACTION
100
2.477-2.5655
0.2123
139
0.1755
2648
X-RAY DIFFRACTION
100
2.5655-2.6681
0.2176
150
0.1787
2644
X-RAY DIFFRACTION
100
2.6681-2.7895
0.2102
153
0.1788
2658
X-RAY DIFFRACTION
100
2.7895-2.9365
0.3035
118
0.19
2692
X-RAY DIFFRACTION
100
2.9365-3.1203
0.2875
144
0.1842
2667
X-RAY DIFFRACTION
100
3.1203-3.3611
0.2295
147
0.1811
2684
X-RAY DIFFRACTION
100
3.3611-3.6989
0.2272
142
0.1736
2694
X-RAY DIFFRACTION
100
3.6989-4.2332
0.2103
140
0.1421
2720
X-RAY DIFFRACTION
100
4.2332-5.3298
0.1674
139
0.1258
2769
X-RAY DIFFRACTION
100
5.3298-33.1914
0.2023
146
0.1655
2880
X-RAY DIFFRACTION
99
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
0.3883
-0.1511
0.1044
0.4904
0.2675
2.3452
0.0215
-0.0059
-0.0642
-0.0242
0.0737
-0.0125
0.336
-0.1809
0.005
0.3255
-0.1345
-0.0334
0.2979
0.0365
0.3071
22.8101
11.3308
15.0781
2
0.4138
-0.2414
-0.5271
0.5465
0.3803
0.9242
-0.142
-0.0288
0.0792
0.2077
0.189
-0.0539
0.0673
-0.032
-0.0015
0.3037
0.0309
0.0122
0.2648
-0.013
0.3061
23.9763
9.9955
57.9147
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid32through352 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid353through593 )
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